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galaxy.datatypes package

Subpackages

• galaxy.datatypes.converters package
  • Submodules
  • galaxy.datatypes.converters.bed_to_gff_converter module
  • galaxy.datatypes.converters.bedgraph_to_array_tree_converter module
  • galaxy.datatypes.converters.bgzip module
  • galaxy.datatypes.converters.cram_to_bam module
  • galaxy.datatypes.converters.fasta_to_len module
  • galaxy.datatypes.converters.fasta_to_tabular_converter module
  • galaxy.datatypes.converters.fastq_to_fqtoc module
  • galaxy.datatypes.converters.fastqsolexa_to_fasta_converter module
  • galaxy.datatypes.converters.fastqsolexa_to_qual_converter module
  • galaxy.datatypes.converters.gff_to_bed_converter module
  • galaxy.datatypes.converters.gff_to_interval_index_converter module
  • galaxy.datatypes.converters.interval_to_bed_converter module
  • galaxy.datatypes.converters.interval_to_bedstrict_converter module
  • galaxy.datatypes.converters.interval_to_coverage module
  • galaxy.datatypes.converters.interval_to_fli module
  • galaxy.datatypes.converters.interval_to_interval_index_converter module
  • galaxy.datatypes.converters.interval_to_tabix_converter module
  • galaxy.datatypes.converters.lped_to_fped_converter module
  • galaxy.datatypes.converters.lped_to_pbed_converter module
  • galaxy.datatypes.converters.maf_to_fasta_converter module
  • galaxy.datatypes.converters.maf_to_interval_converter module
  • galaxy.datatypes.converters.pbed_ldreduced_converter module
  • galaxy.datatypes.converters.pbed_to_lped_converter module
  • galaxy.datatypes.converters.picard_interval_list_to_bed6_converter module
  • galaxy.datatypes.converters.pileup_to_interval_index_converter module
  • galaxy.datatypes.converters.ref_to_seq_taxonomy_converter module
  • galaxy.datatypes.converters.sam_to_bam module
  • galaxy.datatypes.converters.tabular_to_dbnsfp module
  • galaxy.datatypes.converters.vcf_to_interval_index_converter module
  • galaxy.datatypes.converters.vcf_to_vcf_bgzip module
  • galaxy.datatypes.converters.wiggle_to_array_tree_converter module
  • galaxy.datatypes.converters.wiggle_to_simple_converter module
• galaxy.datatypes.dataproviders package
  • Submodules
  • galaxy.datatypes.dataproviders.base module
  • galaxy.datatypes.dataproviders.chunk module
  • galaxy.datatypes.dataproviders.column module
  • galaxy.datatypes.dataproviders.dataset module
  • galaxy.datatypes.dataproviders.decorators module
  • galaxy.datatypes.dataproviders.exceptions module
  • galaxy.datatypes.dataproviders.external module
  • galaxy.datatypes.dataproviders.hierarchy module
  • galaxy.datatypes.dataproviders.line module
• galaxy.datatypes.display_applications package
  • Submodules
  • galaxy.datatypes.display_applications.application module
  • galaxy.datatypes.display_applications.parameters module
  • galaxy.datatypes.display_applications.util module
• galaxy.datatypes.util package
  • Submodules
  • galaxy.datatypes.util.generic_util module
  • galaxy.datatypes.util.gff_util module

Submodules

galaxy.datatypes.annotation module

class galaxy.datatypes.annotation.SnapHmm(**kwd)

Bases: galaxy.datatypes.data.Text

file_ext = 'snaphmm'

edam_data = 'data_1364'

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

sniff_prefix(file_prefix)

SNAP model files start with zoeHMM

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.annotation.Augustus(**kwd)

Bases: galaxy.datatypes.binary.CompressedArchive

Class describing an Augustus prediction model

file_ext = 'augustus'

edam_data = 'data_0950'

compressed = True

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

sniff(filename)

Augustus archives always contain the same files

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

galaxy.datatypes.assembly module

velvet datatypes James E Johnson - University of Minnesota for velvet assembler tool in galaxy

class galaxy.datatypes.assembly.Amos(**kwd)

Bases: galaxy.datatypes.data.Text

Class describing the AMOS assembly file

edam_data = 'data_0925'

edam_format = 'format_3582'

file_ext = 'afg'

sniff_prefix(file_prefix)

Determines whether the file is an amos assembly file format Example:

{CTG
iid:1
eid:1
seq:
CCTCTCCTGTAGAGTTCAACCGA-GCCGGTAGAGTTTTATCA
.
qlt:
DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
.
{TLE
src:1027
off:0
clr:618,0
gap:
250 612
.
}
}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.assembly.Sequences(**kwd)

Bases: galaxy.datatypes.sequence.Fasta

Class describing the Sequences file generated by velveth

edam_data = 'data_0925'

file_ext = 'sequences'

sniff_prefix(file_prefix)

Determines whether the file is a velveth produced fasta format The id line has 3 fields separated by tabs: sequence_name sequence_index category:

>SEQUENCE_0_length_35   1       1
GGATATAGGGCCAACCCAACTCAACGGCCTGTCTT
>SEQUENCE_1_length_35   2       1
CGACGAATGACAGGTCACGAATTTGGCGGGGATTA

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequences (MetadataParameter): Number of sequences, defaults to '0'

sniff(filename)

class galaxy.datatypes.assembly.Roadmaps(**kwd)

Bases: galaxy.datatypes.data.Text

Class describing the Sequences file generated by velveth

edam_format = 'format_2561'

file_ext = 'roadmaps'

sniff_prefix(file_prefix)

Determines whether the file is a velveth produced RoadMap::

142858 21 1 ROADMAP 1 ROADMAP 2 …

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.assembly.Velvet(**kwd)

Bases: galaxy.datatypes.text.Html

composite_type = 'auto_primary_file'

allow_datatype_change = False

file_ext = 'velvet'

__init__(**kwd)

generate_primary_file(dataset=None)

regenerate_primary_file(dataset)

cannot do this until we are setting metadata

set_meta(dataset, **kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for velveth dataset, defaults to 'velvet', paired_end_reads (MetadataParameter): has paired-end reads, defaults to 'False', long_reads (MetadataParameter): has long reads, defaults to 'False', short2_reads (MetadataParameter): has 2nd short reads, defaults to 'False'

galaxy.datatypes.binary module

Binary classes

class galaxy.datatypes.binary.Binary(**kwd)

Bases: galaxy.datatypes.data.Data

Binary data

edam_format = 'format_2333'

static register_sniffable_binary_format(data_type, ext, type_class)

Deprecated method.

static register_unsniffable_binary_ext(ext)

Deprecated method.

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

get_mime()

Returns the mime type of the datatype

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Ab1(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing an ab1 binary sequence file

file_ext = 'ab1'

edam_format = 'format_3000'

edam_data = 'data_0924'

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Idat(**kwd)

Bases: galaxy.datatypes.binary.Binary

Binary data in idat format

file_ext = 'idat'

edam_format = 'format_2058'

edam_data = 'data_2603'

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Cel(**kwd)

Bases: galaxy.datatypes.binary.Binary

Binary data in CEL format.

file_ext = 'cel'

edam_format = 'format_1638'

edam_data = 'data_3110'

sniff(filename)

Try to guess if the file is a CEL file.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.CEL')
>>> Cel().sniff(fname)
True

>>> fname = get_test_fname('drugbank_drugs.mz5')
>>> Cel().sniff(fname)
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.CompressedArchive(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing an compressed binary file This class can be sublass’ed to implement archive filetypes that will not be unpacked by upload.py.

file_ext = 'compressed_archive'

compressed = True

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.DynamicCompressedArchive(**kwd)

Bases: galaxy.datatypes.binary.CompressedArchive

matches_any(target_datatypes)

Treat two aspects of compressed datatypes separately.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.GzDynamicCompressedArchive(**kwd)

Bases: galaxy.datatypes.binary.DynamicCompressedArchive

compressed_format = 'gzip'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Bz2DynamicCompressedArchive(**kwd)

Bases: galaxy.datatypes.binary.DynamicCompressedArchive

compressed_format = 'bz2'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.CompressedZipArchive(**kwd)

Bases: galaxy.datatypes.binary.CompressedArchive

Class describing an compressed binary file This class can be sublass’ed to implement archive filetypes that will not be unpacked by upload.py.

file_ext = 'zip'

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.GenericAsn1Binary(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class for generic ASN.1 binary format

file_ext = 'asn1-binary'

edam_format = 'format_1966'

edam_data = 'data_0849'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.BamNative(**kwd)

Bases: galaxy.datatypes.binary.CompressedArchive

Class describing a BAM binary file that is not necessarily sorted

edam_format = 'format_2572'

edam_data = 'data_0863'

file_ext = 'unsorted.bam'

sort_flag = None

static merge(split_files, output_file)

Merges BAM files

Parameters:

• split_files – List of bam file paths to merge
• output_file – Write merged bam file to this location

init_meta(dataset, copy_from=None)

sniff(filename)

set_meta(dataset, overwrite=True, **kwd)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

to_archive(trans, dataset, name='')

groom_dataset_content(file_name)

Ensures that the BAM file contents are coordinate-sorted. This function is called on an output dataset after the content is initially generated.

get_chunk(trans, dataset, offset=0, ck_size=None)

display_data(trans, dataset, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', bam_version (MetadataParameter): BAM Version, defaults to 'None', sort_order (MetadataParameter): Sort Order, defaults to 'None', read_groups (MetadataParameter): Read Groups, defaults to '[]', reference_names (MetadataParameter): Chromosome Names, defaults to '[]', reference_lengths (MetadataParameter): Chromosome Lengths, defaults to '[]', bam_header (MetadataParameter): Dictionary of BAM Headers, defaults to '{}', columns (MetadataParameter): Number of columns, defaults to '12', column_types (ColumnTypesParameter): Column types, defaults to '['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str']', column_names (MetadataParameter): Column names, defaults to '['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR', 'MRNM', 'MPOS', 'ISIZE', 'SEQ', 'QUAL', 'OPT']'

class galaxy.datatypes.binary.Bam(**kwd)

Bases: galaxy.datatypes.binary.BamNative

Class describing a BAM binary file

edam_format = 'format_2572'

edam_data = 'data_0863'

file_ext = 'bam'

track_type = 'ReadTrack'

data_sources = {'data': 'bai', 'index': 'bigwig'}

dataset_content_needs_grooming(file_name)

Check if file_name is a coordinate-sorted BAM file

set_meta(dataset, overwrite=True, **kwd)

sniff(file_name)

line_dataprovider(*args, **kwargs)

regex_line_dataprovider(*args, **kwargs)

column_dataprovider(*args, **kwargs)

dict_dataprovider(*args, **kwargs)

header_dataprovider(*args, **kwargs)

id_seq_qual_dataprovider(*args, **kwargs)

genomic_region_dataprovider(*args, **kwargs)

genomic_region_dict_dataprovider(*args, **kwargs)

samtools_dataprovider(*args, **kwargs)

Generic samtools interface - all options available through settings.

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'column': <function column_dataprovider at 0x7fbb50a69050>, 'dict': <function dict_dataprovider at 0x7fbb50a691b8>, 'genomic-region': <function genomic_region_dataprovider at 0x7fbb50a695f0>, 'genomic-region-dict': <function genomic_region_dict_dataprovider at 0x7fbb50a69758>, 'header': <function header_dataprovider at 0x7fbb50a69320>, 'id-seq-qual': <function id_seq_qual_dataprovider at 0x7fbb50a69488>, 'line': <function line_dataprovider at 0x7fbb50a6acf8>, 'regex-line': <function regex_line_dataprovider at 0x7fbb50a6ae60>, 'samtools': <function samtools_dataprovider at 0x7fbb50a698c0>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', bam_version (MetadataParameter): BAM Version, defaults to 'None', sort_order (MetadataParameter): Sort Order, defaults to 'None', read_groups (MetadataParameter): Read Groups, defaults to '[]', reference_names (MetadataParameter): Chromosome Names, defaults to '[]', reference_lengths (MetadataParameter): Chromosome Lengths, defaults to '[]', bam_header (MetadataParameter): Dictionary of BAM Headers, defaults to '{}', columns (MetadataParameter): Number of columns, defaults to '12', column_types (ColumnTypesParameter): Column types, defaults to '['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str']', column_names (MetadataParameter): Column names, defaults to '['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR', 'MRNM', 'MPOS', 'ISIZE', 'SEQ', 'QUAL', 'OPT']', bam_index (FileParameter): BAM Index File, defaults to 'None'

class galaxy.datatypes.binary.ProBam(**kwd)

Bases: galaxy.datatypes.binary.Bam

Class describing a BAM binary file - extended for proteomics data

edam_format = 'format_3826'

edam_data = 'data_0863'

file_ext = 'probam'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', bam_version (MetadataParameter): BAM Version, defaults to 'None', sort_order (MetadataParameter): Sort Order, defaults to 'None', read_groups (MetadataParameter): Read Groups, defaults to '[]', reference_names (MetadataParameter): Chromosome Names, defaults to '[]', reference_lengths (MetadataParameter): Chromosome Lengths, defaults to '[]', bam_header (MetadataParameter): Dictionary of BAM Headers, defaults to '{}', columns (MetadataParameter): Number of columns, defaults to '12', column_types (ColumnTypesParameter): Column types, defaults to '['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str']', column_names (MetadataParameter): Column names, defaults to '['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR', 'MRNM', 'MPOS', 'ISIZE', 'SEQ', 'QUAL', 'OPT']', bam_index (FileParameter): BAM Index File, defaults to 'None'

class galaxy.datatypes.binary.BamInputSorted(**kwd)

Bases: galaxy.datatypes.binary.BamNative

sort_flag = '-n'

file_ext = 'qname_input_sorted.bam'

A class for BAM files that can formally be unsorted or queryname sorted. Alignments are either ordered based on the order with which the queries appear when producing the alignment, or ordered by their queryname. This notaby keeps alignments produced by paired end sequencing adjacent.

sniff(file_name)

dataset_content_needs_grooming(file_name)

Groom if the file is coordinate sorted

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', bam_version (MetadataParameter): BAM Version, defaults to 'None', sort_order (MetadataParameter): Sort Order, defaults to 'None', read_groups (MetadataParameter): Read Groups, defaults to '[]', reference_names (MetadataParameter): Chromosome Names, defaults to '[]', reference_lengths (MetadataParameter): Chromosome Lengths, defaults to '[]', bam_header (MetadataParameter): Dictionary of BAM Headers, defaults to '{}', columns (MetadataParameter): Number of columns, defaults to '12', column_types (ColumnTypesParameter): Column types, defaults to '['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str']', column_names (MetadataParameter): Column names, defaults to '['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR', 'MRNM', 'MPOS', 'ISIZE', 'SEQ', 'QUAL', 'OPT']'

class galaxy.datatypes.binary.BamQuerynameSorted(**kwd)

Bases: galaxy.datatypes.binary.BamInputSorted

A class for queryname sorted BAM files.

sort_flag = '-n'

file_ext = 'qname_sorted.bam'

sniff(file_name)

dataset_content_needs_grooming(file_name)

Check if file_name is a queryname-sorted BAM file

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', bam_version (MetadataParameter): BAM Version, defaults to 'None', sort_order (MetadataParameter): Sort Order, defaults to 'None', read_groups (MetadataParameter): Read Groups, defaults to '[]', reference_names (MetadataParameter): Chromosome Names, defaults to '[]', reference_lengths (MetadataParameter): Chromosome Lengths, defaults to '[]', bam_header (MetadataParameter): Dictionary of BAM Headers, defaults to '{}', columns (MetadataParameter): Number of columns, defaults to '12', column_types (ColumnTypesParameter): Column types, defaults to '['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str']', column_names (MetadataParameter): Column names, defaults to '['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR', 'MRNM', 'MPOS', 'ISIZE', 'SEQ', 'QUAL', 'OPT']'

class galaxy.datatypes.binary.CRAM(**kwd)

Bases: galaxy.datatypes.binary.Binary

file_ext = 'cram'

edam_format = 'format_3462'

edam_data = 'format_0863'

set_meta(dataset, overwrite=True, **kwd)

get_cram_version(filename)

set_index_file(dataset, index_file)

set_peek(dataset, is_multi_byte=False)

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', cram_version (MetadataParameter): CRAM Version, defaults to 'None', cram_index (FileParameter): CRAM Index File, defaults to 'None'

class galaxy.datatypes.binary.BaseBcf(**kwd)

Bases: galaxy.datatypes.binary.CompressedArchive

edam_format = 'format_3020'

edam_data = 'data_3498'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Bcf(**kwd)

Bases: galaxy.datatypes.binary.BaseBcf

Class describing a (BGZF-compressed) BCF file

file_ext = 'bcf'

sniff(filename)

set_meta(dataset, overwrite=True, **kwd)

Creates the index for the BCF file.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', bcf_index (FileParameter): BCF Index File, defaults to 'None'

class galaxy.datatypes.binary.BcfUncompressed(**kwd)

Bases: galaxy.datatypes.binary.Bcf

Class describing an uncompressed BCF file

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('1.bcf_uncompressed')
>>> BcfUncompressed().sniff(fname)
True
>>> fname = get_test_fname('1.bcf')
>>> BcfUncompressed().sniff(fname)
False

file_ext = 'bcf_uncompressed'

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', bcf_index (FileParameter): BCF Index File, defaults to 'None'

class galaxy.datatypes.binary.H5(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing an HDF5 file

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.mz5')
>>> H5().sniff(fname)
True
>>> fname = get_test_fname('interval.interval')
>>> H5().sniff(fname)
False

file_ext = 'h5'

edam_format = 'format_3590'

__init__(**kwd)

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Loom(**kwd)

Bases: galaxy.datatypes.binary.H5

Class describing a Loom file: http://loompy.org/

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.loom')
>>> Loom().sniff(fname)
True
>>> fname = get_test_fname('test.mz5')
>>> Loom().sniff(fname)
False

file_ext = 'loom'

edam_format = 'format_3590'

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

set_meta(dataset, overwrite=True, **kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', title (MetadataParameter): title, defaults to '', description (MetadataParameter): description, defaults to '', url (MetadataParameter): url, defaults to '', doi (MetadataParameter): doi, defaults to '', loom_spec_version (MetadataParameter): loom_spec_version, defaults to '', creation_date (MetadataParameter): creation_date, defaults to 'None', shape (ListParameter): shape, defaults to '()', layers_count (MetadataParameter): layers_count, defaults to '0', layers_names (SelectParameter): layers_names, defaults to '[]', row_attrs_count (MetadataParameter): row_attrs_count, defaults to '0', row_attrs_names (SelectParameter): row_attrs_names, defaults to '[]', col_attrs_count (MetadataParameter): col_attrs_count, defaults to '0', col_attrs_names (SelectParameter): col_attrs_names, defaults to '[]', col_graphs_count (MetadataParameter): col_graphs_count, defaults to '0', col_graphs_names (SelectParameter): col_graphs_names, defaults to '[]', row_graphs_count (MetadataParameter): row_graphs_count, defaults to '0', row_graphs_names (SelectParameter): row_graphs_names, defaults to '[]'

class galaxy.datatypes.binary.GmxBinary(**kwd)

Bases: galaxy.datatypes.binary.Binary

Base class for GROMACS binary files - xtc, trr, cpt

magic_number = None

file_ext = ''

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Trr(**kwd)

Bases: galaxy.datatypes.binary.GmxBinary

Class describing an trr file from the GROMACS suite

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('md.trr')
>>> Trr().sniff(fname)
True
>>> fname = get_test_fname('interval.interval')
>>> Trr().sniff(fname)
False

file_ext = 'trr'

magic_number = 1993

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Cpt(**kwd)

Bases: galaxy.datatypes.binary.GmxBinary

Class describing a checkpoint (.cpt) file from the GROMACS suite

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('md.cpt')
>>> Cpt().sniff(fname)
True
>>> fname = get_test_fname('md.trr')
>>> Cpt().sniff(fname)
False

file_ext = 'cpt'

magic_number = 171817

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Xtc(**kwd)

Bases: galaxy.datatypes.binary.GmxBinary

Class describing an xtc file from the GROMACS suite

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('md.xtc')
>>> Xtc().sniff(fname)
True
>>> fname = get_test_fname('md.trr')
>>> Xtc().sniff(fname)
False

file_ext = 'xtc'

magic_number = 1995

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Biom2(**kwd)

Bases: galaxy.datatypes.binary.H5

Class describing a biom2 file (http://biom-format.org/documentation/biom_format.html)

file_ext = 'biom2'

edam_format = 'format_3746'

sniff(filename)

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('biom2_sparse_otu_table_hdf5.biom')
>>> Biom2().sniff(fname)
True
>>> fname = get_test_fname('test.mz5')
>>> Biom2().sniff(fname)
False
>>> fname = get_test_fname('wiggle.wig')
>>> Biom2().sniff(fname)
False

set_meta(dataset, overwrite=True, **kwd)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', id (MetadataParameter): table id, defaults to 'None', format_url (MetadataParameter): format-url, defaults to 'None', format_version (MetadataParameter): format-version, defaults to 'None', format (MetadataParameter): format, defaults to 'None', type (MetadataParameter): table type, defaults to 'None', generated_by (MetadataParameter): generated by, defaults to 'None', creation_date (MetadataParameter): creation date, defaults to 'None', nnz (MetadataParameter): nnz: The number of non-zero elements in the table, defaults to '-1', shape (MetadataParameter): shape: The number of rows and columns in the dataset, defaults to '()'

class galaxy.datatypes.binary.Cool(**kwd)

Bases: galaxy.datatypes.binary.H5

Class describing the cool format (https://github.com/mirnylab/cooler)

file_ext = 'cool'

sniff(filename)

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('matrix.cool')
>>> Cool().sniff(fname)
True
>>> fname = get_test_fname('test.mz5')
>>> Cool().sniff(fname)
False
>>> fname = get_test_fname('wiggle.wig')
>>> Cool().sniff(fname)
False
>>> fname = get_test_fname('biom2_sparse_otu_table_hdf5.biom')
>>> Cool().sniff(fname)
False

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Scf(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing an scf binary sequence file

edam_format = 'format_1632'

edam_data = 'data_0924'

file_ext = 'scf'

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Sff(**kwd)

Bases: galaxy.datatypes.binary.Binary

Standard Flowgram Format (SFF)

edam_format = 'format_3284'

edam_data = 'data_0924'

file_ext = 'sff'

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.BigWig(**kwd)

Bases: galaxy.datatypes.binary.Binary

Accessing binary BigWig files from UCSC. The supplemental info in the paper has the binary details: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq351v1

edam_format = 'format_3006'

edam_data = 'data_3002'

file_ext = 'bigwig'

track_type = 'LineTrack'

data_sources = {'data_standalone': 'bigwig'}

__init__(**kwd)

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.BigBed(**kwd)

Bases: galaxy.datatypes.binary.BigWig

BigBed support from UCSC.

edam_format = 'format_3004'

edam_data = 'data_3002'

file_ext = 'bigbed'

data_sources = {'data_standalone': 'bigbed'}

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.TwoBit(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing a TwoBit format nucleotide file

edam_format = 'format_3009'

edam_data = 'data_0848'

file_ext = 'twobit'

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.SQlite(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing a Sqlite database

file_ext = 'sqlite'

edam_format = 'format_3621'

init_meta(dataset, copy_from=None)

set_meta(dataset, overwrite=True, **kwd)

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

sqlite_dataprovider(*args, **kwargs)

sqlite_datatableprovider(*args, **kwargs)

sqlite_datadictprovider(*args, **kwargs)

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'sqlite': <function sqlite_dataprovider at 0x7fbb50aa20c8>, 'sqlite-dict': <function sqlite_datadictprovider at 0x7fbb50aa2398>, 'sqlite-table': <function sqlite_datatableprovider at 0x7fbb50aa2230>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', tables (ListParameter): Database Tables, defaults to '[]', table_columns (DictParameter): Database Table Columns, defaults to '{}', table_row_count (DictParameter): Database Table Row Count, defaults to '{}'

class galaxy.datatypes.binary.GeminiSQLite(**kwd)

Bases: galaxy.datatypes.binary.SQlite

Class describing a Gemini Sqlite database

file_ext = 'gemini.sqlite'

edam_format = 'format_3622'

edam_data = 'data_3498'

set_meta(dataset, overwrite=True, **kwd)

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', tables (ListParameter): Database Tables, defaults to '[]', table_columns (DictParameter): Database Table Columns, defaults to '{}', table_row_count (DictParameter): Database Table Row Count, defaults to '{}', gemini_version (MetadataParameter): Gemini Version, defaults to '0.10.0'

class galaxy.datatypes.binary.CuffDiffSQlite(**kwd)

Bases: galaxy.datatypes.binary.SQlite

Class describing a CuffDiff SQLite database

file_ext = 'cuffdiff.sqlite'

edam_format = 'format_3621'

set_meta(dataset, overwrite=True, **kwd)

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', tables (ListParameter): Database Tables, defaults to '[]', table_columns (DictParameter): Database Table Columns, defaults to '{}', table_row_count (DictParameter): Database Table Row Count, defaults to '{}', cuffdiff_version (MetadataParameter): CuffDiff Version, defaults to '2.2.1', genes (MetadataParameter): Genes, defaults to '[]', samples (MetadataParameter): Samples, defaults to '[]'

class galaxy.datatypes.binary.MzSQlite(**kwd)

Bases: galaxy.datatypes.binary.SQlite

Class describing a Proteomics Sqlite database

file_ext = 'mz.sqlite'

set_meta(dataset, overwrite=True, **kwd)

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', tables (ListParameter): Database Tables, defaults to '[]', table_columns (DictParameter): Database Table Columns, defaults to '{}', table_row_count (DictParameter): Database Table Row Count, defaults to '{}'

class galaxy.datatypes.binary.BlibSQlite(**kwd)

Bases: galaxy.datatypes.binary.SQlite

Class describing a Proteomics Spectral Library Sqlite database

file_ext = 'blib'

set_meta(dataset, overwrite=True, **kwd)

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', tables (ListParameter): Database Tables, defaults to '[]', table_columns (DictParameter): Database Table Columns, defaults to '{}', table_row_count (DictParameter): Database Table Row Count, defaults to '{}', blib_version (MetadataParameter): Blib Version, defaults to '1.8'

class galaxy.datatypes.binary.IdpDB(**kwd)

Bases: galaxy.datatypes.binary.SQlite

Class describing an IDPicker 3 idpDB (sqlite) database

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.idpDB')
>>> IdpDB().sniff(fname)
True
>>> fname = get_test_fname('interval.interval')
>>> IdpDB().sniff(fname)
False

file_ext = 'idpdb'

set_meta(dataset, overwrite=True, **kwd)

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', tables (ListParameter): Database Tables, defaults to '[]', table_columns (DictParameter): Database Table Columns, defaults to '{}', table_row_count (DictParameter): Database Table Row Count, defaults to '{}'

class galaxy.datatypes.binary.GAFASQLite(**kwd)

Bases: galaxy.datatypes.binary.SQlite

Class describing a GAFA SQLite database

file_ext = 'gafa.sqlite'

set_meta(dataset, overwrite=True, **kwd)

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', tables (ListParameter): Database Tables, defaults to '[]', table_columns (DictParameter): Database Table Columns, defaults to '{}', table_row_count (DictParameter): Database Table Row Count, defaults to '{}', gafa_schema_version (MetadataParameter): GAFA schema version, defaults to '0.1.0'

class galaxy.datatypes.binary.Xlsx(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class for Excel 2007 (xlsx) files

file_ext = 'xlsx'

compressed = True

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.ExcelXls(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing an Excel (xls) file

file_ext = 'excel.xls'

edam_format = 'format_3468'

sniff(filename)

get_mime()

Returns the mime type of the datatype

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Sra(**kwd)

Bases: galaxy.datatypes.binary.Binary

Sequence Read Archive (SRA) datatype originally from mdshw5/sra-tools-galaxy

file_ext = 'sra'

sniff(filename)

The first 8 bytes of any NCBI sra file is ‘NCBI.sra’, and the file is binary. For details about the format, see http://www.ncbi.nlm.nih.gov/books/n/helpsra/SRA_Overview_BK/#SRA_Overview_BK.4_SRA_Data_Structure

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.RData(**kwd)

Bases: galaxy.datatypes.binary.Binary

Generic R Data file datatype implementation

file_ext = 'rdata'

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.OxliBinary(**kwd)

Bases: galaxy.datatypes.binary.Binary

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.OxliCountGraph(**kwd)

Bases: galaxy.datatypes.binary.OxliBinary

OxliCountGraph starts with “OXLI” + one byte version number + 8-bit binary ‘1’ Test file generated via:

load-into-counting.py --n_tables 1 --max-tablesize 1 \
    oxli_countgraph.oxlicg khmer/tests/test-data/100-reads.fq.bz2

using khmer 2.0

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('sequence.csfasta')
>>> OxliCountGraph().sniff(fname)
False
>>> fname = get_test_fname("oxli_countgraph.oxlicg")
>>> OxliCountGraph().sniff(fname)
True

file_ext = 'oxlicg'

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.OxliNodeGraph(**kwd)

Bases: galaxy.datatypes.binary.OxliBinary

OxliNodeGraph starts with “OXLI” + one byte version number + 8-bit binary ‘2’ Test file generated via:

load-graph.py --n_tables 1 --max-tablesize 1 oxli_nodegraph.oxling \
    khmer/tests/test-data/100-reads.fq.bz2

using khmer 2.0

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('sequence.csfasta')
>>> OxliNodeGraph().sniff(fname)
False
>>> fname = get_test_fname("oxli_nodegraph.oxling")
>>> OxliNodeGraph().sniff(fname)
True

file_ext = 'oxling'

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.OxliTagSet(**kwd)

Bases: galaxy.datatypes.binary.OxliBinary

OxliTagSet starts with “OXLI” + one byte version number + 8-bit binary ‘3’ Test file generated via:

load-graph.py --n_tables 1 --max-tablesize 1 oxli_nodegraph.oxling \
    khmer/tests/test-data/100-reads.fq.bz2;
mv oxli_nodegraph.oxling.tagset oxli_tagset.oxlits

using khmer 2.0

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('sequence.csfasta')
>>> OxliTagSet().sniff(fname)
False
>>> fname = get_test_fname("oxli_tagset.oxlits")
>>> OxliTagSet().sniff(fname)
True

file_ext = 'oxlits'

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.OxliStopTags(**kwd)

Bases: galaxy.datatypes.binary.OxliBinary

OxliStopTags starts with “OXLI” + one byte version number + 8-bit binary ‘4’ Test file adapted from khmer 2.0’s “khmer/tests/test-data/goodversion-k32.stoptags”

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('sequence.csfasta')
>>> OxliStopTags().sniff(fname)
False
>>> fname = get_test_fname("oxli_stoptags.oxlist")
>>> OxliStopTags().sniff(fname)
True

file_ext = 'oxlist'

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.OxliSubset(**kwd)

Bases: galaxy.datatypes.binary.OxliBinary

OxliSubset starts with “OXLI” + one byte version number + 8-bit binary ‘5’ Test file generated via:

load-graph.py -k 20 example tests/test-data/random-20-a.fa;
partition-graph.py example;
mv example.subset.0.pmap oxli_subset.oxliss

using khmer 2.0

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('sequence.csfasta')
>>> OxliSubset().sniff(fname)
False
>>> fname = get_test_fname("oxli_subset.oxliss")
>>> OxliSubset().sniff(fname)
True

file_ext = 'oxliss'

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.OxliGraphLabels(**kwd)

Bases: galaxy.datatypes.binary.OxliBinary

OxliGraphLabels starts with “OXLI” + one byte version number + 8-bit binary ‘6’ Test file generated via:

python -c "from khmer import GraphLabels; \
    gl = GraphLabels(20, 1e7, 4); \
    gl.consume_fasta_and_tag_with_labels('tests/test-data/test-labels.fa'); \
    gl.save_labels_and_tags('oxli_graphlabels.oxligl')"

using khmer 2.0

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('sequence.csfasta')
>>> OxliGraphLabels().sniff(fname)
False
>>> fname = get_test_fname("oxli_graphlabels.oxligl")
>>> OxliGraphLabels().sniff(fname)
True

file_ext = 'oxligl'

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.PostgresqlArchive(**kwd)

Bases: galaxy.datatypes.binary.CompressedArchive

Class describing a Postgresql database packed into a tar archive

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('postgresql_fake.tar.bz2')
>>> PostgresqlArchive().sniff(fname)
True
>>> fname = get_test_fname('test.fast5.tar')
>>> PostgresqlArchive().sniff(fname)
False

file_ext = 'postgresql'

set_meta(dataset, overwrite=True, **kwd)

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', version (MetadataParameter): PostgreSQL database version, defaults to 'None'

class galaxy.datatypes.binary.Fast5Archive(**kwd)

Bases: galaxy.datatypes.binary.CompressedArchive

Class describing a FAST5 archive

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.fast5.tar')
>>> Fast5Archive().sniff(fname)
True

file_ext = 'fast5.tar'

set_meta(dataset, overwrite=True, **kwd)

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', fast5_count (MetadataParameter): Read Count, defaults to '0'

class galaxy.datatypes.binary.Fast5ArchiveGz(**kwd)

Bases: galaxy.datatypes.binary.Fast5Archive

Class describing a gzip-compressed FAST5 archive

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.fast5.tar.gz')
>>> Fast5ArchiveGz().sniff(fname)
True
>>> fname = get_test_fname('test.fast5.tar.bz2')
>>> Fast5ArchiveGz().sniff(fname)
False
>>> fname = get_test_fname('test.fast5.tar')
>>> Fast5ArchiveGz().sniff(fname)
False

file_ext = 'fast5.tar.gz'

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', fast5_count (MetadataParameter): Read Count, defaults to '0'

class galaxy.datatypes.binary.Fast5ArchiveBz2(**kwd)

Bases: galaxy.datatypes.binary.Fast5Archive

Class describing a bzip2-compressed FAST5 archive

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.fast5.tar.bz2')
>>> Fast5ArchiveBz2().sniff(fname)
True
>>> fname = get_test_fname('test.fast5.tar.gz')
>>> Fast5ArchiveBz2().sniff(fname)
False
>>> fname = get_test_fname('test.fast5.tar')
>>> Fast5ArchiveBz2().sniff(fname)
False

file_ext = 'fast5.tar.bz2'

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', fast5_count (MetadataParameter): Read Count, defaults to '0'

class galaxy.datatypes.binary.SearchGuiArchive(**kwd)

Bases: galaxy.datatypes.binary.CompressedArchive

Class describing a SearchGUI archive

file_ext = 'searchgui_archive'

set_meta(dataset, overwrite=True, **kwd)

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', searchgui_version (MetadataParameter): SearchGui Version, defaults to '1.28.0', searchgui_major_version (MetadataParameter): SearchGui Major Version, defaults to '1'

class galaxy.datatypes.binary.NetCDF(**kwd)

Bases: galaxy.datatypes.binary.Binary

Binary data in netCDF format

file_ext = 'netcdf'

edam_format = 'format_3650'

edam_data = 'data_0943'

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Dcd(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing a dcd file from the CHARMM molecular simulation program

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test_glucose_vacuum.dcd')
>>> Dcd().sniff(fname)
True
>>> fname = get_test_fname('interval.interval')
>>> Dcd().sniff(fname)
False

file_ext = 'dcd'

edam_data = 'data_3842'

__init__(**kwd)

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.Vel(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing a velocity file from the CHARMM molecular simulation program

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test_charmm.vel')
>>> Vel().sniff(fname)
True
>>> fname = get_test_fname('interval.interval')
>>> Vel().sniff(fname)
False

file_ext = 'vel'

__init__(**kwd)

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.DAA(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing an DAA (diamond alignment archive) file >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname(‘diamond.daa’) >>> DAA().sniff(fname) True >>> fname = get_test_fname(‘interval.interval’) >>> DAA().sniff(fname) False

file_ext = 'daa'

__init__(**kwd)

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.DMND(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing an DMND file >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname(‘diamond_db.dmnd’) >>> DMND().sniff(fname) True >>> fname = get_test_fname(‘interval.interval’) >>> DMND().sniff(fname) False

file_ext = 'dmnd'

__init__(**kwd)

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.binary.ICM(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing an ICM (interpolated context model) file, used by Glimmer

file_ext = 'icm'

edam_data = 'data_0950'

set_peek(dataset, is_multi_byte=False)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

sniff(dataset)

galaxy.datatypes.blast module

NCBI BLAST datatypes.

Covers the blastxml format and the BLAST databases.

class galaxy.datatypes.blast.BlastXml(**kwd)

Bases: galaxy.datatypes.xml.GenericXml

NCBI Blast XML Output data

file_ext = 'blastxml'

edam_format = 'format_3331'

edam_data = 'data_0857'

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

sniff_prefix(file_prefix)

Determines whether the file is blastxml

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('megablast_xml_parser_test1.blastxml')
>>> BlastXml().sniff(fname)
True
>>> fname = get_test_fname('tblastn_four_human_vs_rhodopsin.xml')
>>> BlastXml().sniff(fname)
True
>>> fname = get_test_fname('interval.interval')
>>> BlastXml().sniff(fname)
False

static merge(split_files, output_file)

Merging multiple XML files is non-trivial and must be done in subclasses.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.blast.BlastNucDb(**kwd)

Bases: galaxy.datatypes.blast._BlastDb, galaxy.datatypes.data.Data

Class for nucleotide BLAST database files.

file_ext = 'blastdbn'

allow_datatype_change = False

composite_type = 'basic'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.blast.BlastProtDb(**kwd)

Bases: galaxy.datatypes.blast._BlastDb, galaxy.datatypes.data.Data

Class for protein BLAST database files.

file_ext = 'blastdbp'

allow_datatype_change = False

composite_type = 'basic'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.blast.BlastDomainDb(**kwd)

Bases: galaxy.datatypes.blast._BlastDb, galaxy.datatypes.data.Data

Class for domain BLAST database files.

file_ext = 'blastdbd'

allow_datatype_change = False

composite_type = 'basic'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

galaxy.datatypes.checkers module

Module proxies galaxy.util.checkers for backward compatibility.

External datatypes may make use of these functions.

galaxy.datatypes.checkers.check_binary(name, file_path=True)

galaxy.datatypes.checkers.check_bz2(file_path, check_content=True)

galaxy.datatypes.checkers.check_gzip(file_path, check_content=True)

galaxy.datatypes.checkers.check_html(file_path, chunk=None)

galaxy.datatypes.checkers.check_image(file_path)

Simple wrapper around image_type to yield a True/False verdict

galaxy.datatypes.checkers.check_zip(file_path, check_content=True, files=1)

galaxy.datatypes.checkers.is_gzip(file_path)

galaxy.datatypes.checkers.is_bz2(file_path)

galaxy.datatypes.chrominfo module

class galaxy.datatypes.chrominfo.ChromInfo(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'len'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', chrom (ColumnParameter): Chrom column, defaults to '1', length (ColumnParameter): Length column, defaults to '2'

galaxy.datatypes.constructive_solid_geometry module

Constructive Solid Geometry file formats.

class galaxy.datatypes.constructive_solid_geometry.Ply(**kwd)

Bases: object

The PLY format describes an object as a collection of vertices, faces and other elements, along with properties such as color and normal direction that can be attached to these elements. A PLY file contains the description of exactly one object.

subtype = ''

__init__(**kwd)

sniff_prefix(file_prefix)

The structure of a typical PLY file: Header, Vertex List, Face List, (lists of other elements)

set_meta(dataset, **kwd)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

sniff(filename)

class galaxy.datatypes.constructive_solid_geometry.PlyAscii(**kwd)

Bases: galaxy.datatypes.constructive_solid_geometry.Ply, galaxy.datatypes.data.Text

file_ext = 'plyascii'

subtype = 'ascii'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', file_format (MetadataParameter): File format, defaults to 'None', vertex (MetadataParameter): Vertex, defaults to 'None', face (MetadataParameter): Face, defaults to 'None', other_elements (MetadataParameter): Other elements, defaults to '[]'

class galaxy.datatypes.constructive_solid_geometry.PlyBinary(**kwd)

Bases: galaxy.datatypes.constructive_solid_geometry.Ply, galaxy.datatypes.binary.Binary

file_ext = 'plybinary'

subtype = 'binary'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', file_format (MetadataParameter): File format, defaults to 'None', vertex (MetadataParameter): Vertex, defaults to 'None', face (MetadataParameter): Face, defaults to 'None', other_elements (MetadataParameter): Other elements, defaults to '[]'

class galaxy.datatypes.constructive_solid_geometry.Vtk(**kwd)

Bases: object

The Visualization Toolkit provides a number of source and writer objects to read and write popular data file formats. The Visualization Toolkit also provides some of its own file formats.

There are two different styles of file formats available in VTK. The simplest are the legacy, serial formats that are easy to read and write either by hand or programmatically. However, these formats are less flexible than the XML based file formats which support random access, parallel I/O, and portable data compression and are preferred to the serial VTK file formats whenever possible.

All keyword phrases are written in ASCII form whether the file is binary or ASCII. The binary section of the file (if in binary form) is the data proper; i.e., the numbers that define points coordinates, scalars, cell indices, and so forth.

Binary data must be placed into the file immediately after the newline (‘\n’) character from the previous ASCII keyword and parameter sequence.

TODO: only legacy formats are currently supported and support for XML formats should be added.

subtype = ''

__init__(**kwd)

sniff_prefix(file_prefix)

VTK files can be either ASCII or binary, with two different styles of file formats: legacy or XML. We’ll assume if the file contains a valid VTK header, then it is a valid VTK file.

set_meta(dataset, **kwd)

set_initial_metadata(i, line, dataset)

set_structure_metadata(line, dataset, dataset_type)

The fourth part of legacy VTK files is the dataset structure. The geometry part describes the geometry and topology of the dataset. This part begins with a line containing the keyword DATASET followed by a keyword describing the type of dataset. Then, depending upon the type of dataset, other keyword/ data combinations define the actual data.

get_blurb(dataset)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

sniff(filename)

class galaxy.datatypes.constructive_solid_geometry.VtkAscii(**kwd)

Bases: galaxy.datatypes.constructive_solid_geometry.Vtk, galaxy.datatypes.data.Text

file_ext = 'vtkascii'

subtype = 'ASCII'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', vtk_version (MetadataParameter): Vtk version, defaults to 'None', file_format (MetadataParameter): File format, defaults to 'None', dataset_type (MetadataParameter): Dataset type, defaults to 'None', dimensions (MetadataParameter): Dimensions, defaults to '[]', origin (MetadataParameter): Origin, defaults to '[]', spacing (MetadataParameter): Spacing, defaults to '[]', points (MetadataParameter): Points, defaults to 'None', vertices (MetadataParameter): Vertices, defaults to 'None', lines (MetadataParameter): Lines, defaults to 'None', polygons (MetadataParameter): Polygons, defaults to 'None', triangle_strips (MetadataParameter): Triangle strips, defaults to 'None', cells (MetadataParameter): Cells, defaults to 'None', field_names (MetadataParameter): Field names, defaults to '[]', field_components (MetadataParameter): Field names and components, defaults to '{}'

class galaxy.datatypes.constructive_solid_geometry.VtkBinary(**kwd)

Bases: galaxy.datatypes.constructive_solid_geometry.Vtk, galaxy.datatypes.binary.Binary

file_ext = 'vtkbinary'

subtype = 'BINARY'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', vtk_version (MetadataParameter): Vtk version, defaults to 'None', file_format (MetadataParameter): File format, defaults to 'None', dataset_type (MetadataParameter): Dataset type, defaults to 'None', dimensions (MetadataParameter): Dimensions, defaults to '[]', origin (MetadataParameter): Origin, defaults to '[]', spacing (MetadataParameter): Spacing, defaults to '[]', points (MetadataParameter): Points, defaults to 'None', vertices (MetadataParameter): Vertices, defaults to 'None', lines (MetadataParameter): Lines, defaults to 'None', polygons (MetadataParameter): Polygons, defaults to 'None', triangle_strips (MetadataParameter): Triangle strips, defaults to 'None', cells (MetadataParameter): Cells, defaults to 'None', field_names (MetadataParameter): Field names, defaults to '[]', field_components (MetadataParameter): Field names and components, defaults to '{}'

class galaxy.datatypes.constructive_solid_geometry.STL(**kwd)

Bases: galaxy.datatypes.data.Data

file_ext = 'stl'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

galaxy.datatypes.constructive_solid_geometry.get_next_line(fh)

galaxy.datatypes.coverage module

Coverage datatypes

class galaxy.datatypes.coverage.LastzCoverage(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'coverage'

get_track_resolution(dataset, start, end)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '3', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', chromCol (ColumnParameter): Chrom column, defaults to '1', positionCol (ColumnParameter): Position column, defaults to '2', forwardCol (ColumnParameter): Forward or aggregate read column, defaults to '3', reverseCol (ColumnParameter): Optional reverse read column, defaults to 'None'

galaxy.datatypes.data module

class galaxy.datatypes.data.DataMeta(name, bases, dict_)

Bases: abc.ABCMeta

Metaclass for Data class. Sets up metadata spec.

__init__(name, bases, dict_)

class galaxy.datatypes.data.Data(**kwd)

Bases: object

Base class for all datatypes. Implements basic interfaces as well as class methods for metadata.

>>> class DataTest( Data ):
...     MetadataElement( name="test" )
...
>>> DataTest.metadata_spec.test.name
'test'
>>> DataTest.metadata_spec.test.desc
'test'
>>> type( DataTest.metadata_spec.test.param )
<class 'galaxy.model.metadata.MetadataParameter'>

edam_data = 'data_0006'

edam_format = 'format_1915'

file_ext = 'data'

CHUNKABLE = False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

Dictionary of metadata fields for this datatype

copy_safe_peek = True

is_binary = True

allow_datatype_change = True

composite_type = None

primary_file_name = 'index'

track_type = None

data_sources = {}

__init__(**kwd)

Initialize the datatype

supported_display_apps = {}

composite_files = {}

get_raw_data(dataset)

Returns the full data. To stream it open the file_name and read/write as needed

dataset_content_needs_grooming(file_name)

This function is called on an output dataset file after the content is initially generated.

groom_dataset_content(file_name)

This function is called on an output dataset file if dataset_content_needs_grooming returns True.

init_meta(dataset, copy_from=None)

set_meta(dataset, overwrite=True, **kwd)

Unimplemented method, allows guessing of metadata from contents of file

missing_meta(dataset, check=[], skip=[])

Checks for empty metadata values, Returns True if non-optional metadata is missing Specifying a list of ‘check’ values will only check those names provided; when used, optionality is ignored Specifying a list of ‘skip’ items will return True even when a named metadata value is missing

set_max_optional_metadata_filesize(max_value)

get_max_optional_metadata_filesize()

max_optional_metadata_filesize

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

Parameters:is_multi_byte (bool) – deprecated

display_peek(dataset)

Create HTML table, used for displaying peek

to_archive(trans, dataset, name='')

Collect archive paths and file handles that need to be exported when archiving dataset.

Parameters:

• dataset – HistoryDatasetAssociation
• name – archive name, in collection context corresponds to collection name(s) and element_identifier, joined by ‘/’, e.g ‘fastq_collection/sample1/forward’

display_data(trans, data, preview=False, filename=None, to_ext=None, **kwd)

Displays data in central pane if preview is True, else handles download.

Datatypes should be very careful if overridding this method and this interface between datatypes and Galaxy will likely change.

TOOD: Document alternatives to overridding this method (data providers?).

display_name(dataset)

Returns formatted html of dataset name

display_info(dataset)

Returns formatted html of dataset info

validate(dataset)

Unimplemented validate, return no exceptions

repair_methods(dataset)

Unimplemented method, returns dict with method/option for repairing errors

get_mime()

Returns the mime type of the datatype

add_display_app(app_id, label, file_function, links_function)

Adds a display app to the datatype. app_id is a unique id label is the primary display label, e.g., display at ‘UCSC’ file_function is a string containing the name of the function that returns a properly formatted display links_function is a string containing the name of the function that returns a list of (link_name,link)

remove_display_app(app_id)

Removes a display app from the datatype

clear_display_apps()

add_display_application(display_application)

New style display applications

get_display_application(key, default=None)

get_display_applications_by_dataset(dataset, trans)

get_display_types()

Returns display types available

get_display_label(type)

Returns primary label for display app

as_display_type(dataset, type, **kwd)

Returns modified file contents for a particular display type

get_display_links(dataset, type, app, base_url, target_frame='_blank', **kwd)

Returns a list of tuples of (name, link) for a particular display type. No check on ‘access’ permissions is done here - if you can view the dataset, you can also save it or send it to a destination outside of Galaxy, so Galaxy security restrictions do not apply anyway.

get_converter_types(original_dataset, datatypes_registry)

Returns available converters by type for this dataset

find_conversion_destination(dataset, accepted_formats, datatypes_registry, **kwd)

Returns ( target_ext, existing converted dataset )

convert_dataset(trans, original_dataset, target_type, return_output=False, visible=True, deps=None, target_context=None, history=None)

This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure.

after_setting_metadata(dataset)

This function is called on the dataset after metadata is set.

before_setting_metadata(dataset)

This function is called on the dataset before metadata is set.

add_composite_file(name, **kwds)

writable_files

get_composite_files(dataset=None)

generate_primary_file(dataset=None)

has_resolution

matches_any(target_datatypes)

Check if this datatype is of any of the target_datatypes or is a subtype thereof.

static merge(split_files, output_file)

Merge files with copy.copyfileobj() will not hit the max argument limitation of cat. gz and bz2 files are also working.

get_visualizations(dataset)

Returns a list of visualizations for datatype.

has_dataprovider(data_format)

Returns True if data_format is available in dataproviders.

dataprovider(dataset, data_format, **settings)

Base dataprovider factory for all datatypes that returns the proper provider for the given data_format or raises a NoProviderAvailable.

base_dataprovider(*args, **kwargs)

chunk_dataprovider(*args, **kwargs)

chunk64_dataprovider(*args, **kwargs)

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>}

class galaxy.datatypes.data.Text(**kwd)

Bases: galaxy.datatypes.data.Data

edam_format = 'format_2330'

file_ext = 'txt'

line_class = 'line'

is_binary = False

get_mime()

Returns the mime type of the datatype

set_meta(dataset, **kwd)

Set the number of lines of data in dataset.

estimate_file_lines(dataset)

Perform a rough estimate by extrapolating number of lines from a small read.

count_data_lines(dataset)

Count the number of lines of data in dataset, skipping all blank lines and comments.

set_peek(dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=None, line_wrap=True)

Set the peek. This method is used by various subclasses of Text.

classmethod split(input_datasets, subdir_generator_function, split_params)

Split the input files by line.

line_dataprovider(*args, **kwargs)

Returns an iterator over the dataset’s lines (that have been stripped) optionally excluding blank lines and lines that start with a comment character.

regex_line_dataprovider(*args, **kwargs)

Returns an iterator over the dataset’s lines optionally including/excluding lines that match one or more regex filters.

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.data.GenericAsn1(**kwd)

Bases: galaxy.datatypes.data.Text

Class for generic ASN.1 text format

edam_data = 'data_0849'

edam_format = 'format_1966'

file_ext = 'asn1'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.data.LineCount(**kwd)

Bases: galaxy.datatypes.data.Text

Dataset contains a single line with a single integer that denotes the line count for a related dataset. Used for custom builds.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.data.Newick(**kwd)

Bases: galaxy.datatypes.data.Text

New Hampshire/Newick Format

edam_data = 'data_0872'

edam_format = 'format_1910'

file_ext = 'newick'

__init__(**kwd)

Initialize foobar datatype

init_meta(dataset, copy_from=None)

sniff(filename)

Returning false as the newick format is too general and cannot be sniffed.

get_visualizations(dataset)

Returns a list of visualizations for datatype.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.data.Nexus(**kwd)

Bases: galaxy.datatypes.data.Text

Nexus format as used By Paup, Mr Bayes, etc

edam_data = 'data_0872'

edam_format = 'format_1912'

file_ext = 'nex'

__init__(**kwd)

Initialize foobar datatype

init_meta(dataset, copy_from=None)

sniff_prefix(file_prefix)

All Nexus Files Simply puts a ‘#NEXUS’ in its first line

get_visualizations(dataset)

Returns a list of visualizations for datatype.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

galaxy.datatypes.data.get_test_fname(fname)

Returns test data filename

galaxy.datatypes.data.get_file_peek(file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skipchars=None, line_wrap=True)

Returns the first LINE_COUNT lines wrapped to WIDTH.

Parameters:is_multi_byte (bool) – deprecated

>>> fname = get_test_fname('4.bed')
>>> assert get_file_peek(fname, LINE_COUNT=1) == u'chr22\t30128507\t31828507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n'

galaxy.datatypes.genetics module

rgenetics datatypes Use at your peril Ross Lazarus for the rgenetics and galaxy projects

genome graphs datatypes derived from Interval datatypes genome graphs datasets have a header row with appropriate columnames The first column is always the marker - eg columname = rs, first row= rs12345 if the rows are snps subsequent row values are all numeric ! Will fail if any non numeric (eg ‘+’ or ‘NA’) values ross lazarus for rgenetics august 20 2007

class galaxy.datatypes.genetics.GenomeGraphs(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

Tab delimited data containing a marker id and any number of numeric values

file_ext = 'gg'

__init__(**kwd)

Initialize gg datatype, by adding UCSC display apps

set_meta(dataset, **kwd)

as_ucsc_display_file(dataset, **kwd)

Returns file

ucsc_links(dataset, type, app, base_url)

from the ever-helpful angie hinrichs angie@soe.ucsc.edu a genome graphs call looks like this

http://genome.ucsc.edu/cgi-bin/hgGenome?clade=mammal&org=Human&db=hg18&hgGenome_dataSetName=dname &hgGenome_dataSetDescription=test&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess &hgGenome_columnLabels=best%20guess&hgGenome_maxVal=&hgGenome_labelVals= &hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=http://galaxy.esphealth.org/datasets/333/display/index &hgGenome_doSubmitUpload=submit

Galaxy gives this for an interval file

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:1-1000&hgt.customText= http%3A%2F%2Fgalaxy.esphealth.org%2Fdisplay_as%3Fid%3D339%26display_app%3Ducsc

make_html_table(dataset, skipchars=[])

Create HTML table, used for displaying peek

validate(dataset)

Validate a gg file - all numeric after header row

sniff_prefix(file_prefix)

Determines whether the file is in gg format

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'test_space.txt' )
>>> GenomeGraphs().sniff( fname )
False
>>> fname = get_test_fname( '1.gg' )
>>> GenomeGraphs().sniff( fname )
True

get_mime()

Returns the mime type of the datatype

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '3', column_types (MetadataParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', markerCol (ColumnParameter): Marker ID column, defaults to '1'

sniff(filename)

class galaxy.datatypes.genetics.rgTabList(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

for sampleid and for featureid lists of exclusions or inclusions in the clean tool featureid subsets on statistical criteria -> specialized display such as gg

file_ext = 'rgTList'

__init__(**kwd)

Initialize featurelistt datatype

display_peek(dataset)

Returns formated html of peek

get_mime()

Returns the mime type of the datatype

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.genetics.rgSampleList(**kwd)

Bases: galaxy.datatypes.genetics.rgTabList

for sampleid exclusions or inclusions in the clean tool output from QC eg excess het, gender error, ibd pair member,eigen outlier,excess mendel errors,… since they can be uploaded, should be flexible but they are persistent at least same infrastructure for expression?

file_ext = 'rgSList'

__init__(**kwd)

Initialize samplelist datatype

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.genetics.rgFeatureList(**kwd)

Bases: galaxy.datatypes.genetics.rgTabList

for featureid lists of exclusions or inclusions in the clean tool output from QC eg low maf, high missingness, bad hwe in controls, excess mendel errors,… featureid subsets on statistical criteria -> specialized display such as gg same infrastructure for expression?

file_ext = 'rgFList'

__init__(**kwd)

Initialize featurelist datatype

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.genetics.Rgenetics(**kwd)

Bases: galaxy.datatypes.text.Html

base class to use for rgenetics datatypes derived from html - composite datatype elements stored in extra files path

composite_type = 'auto_primary_file'

allow_datatype_change = False

file_ext = 'rgenetics'

generate_primary_file(dataset=None)

regenerate_primary_file(dataset)

cannot do this until we are setting metadata

get_mime()

Returns the mime type of the datatype

set_meta(dataset, **kwd)

for lped/pbed eg

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for all transformed versions of this genetic dataset, defaults to 'RgeneticsData'

class galaxy.datatypes.genetics.SNPMatrix(**kwd)

Bases: galaxy.datatypes.genetics.Rgenetics

BioC SNPMatrix Rgenetics data collections

file_ext = 'snpmatrix'

set_peek(dataset, **kwd)

sniff(filename)

need to check the file header hex code

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for all transformed versions of this genetic dataset, defaults to 'RgeneticsData'

class galaxy.datatypes.genetics.Lped(**kwd)

Bases: galaxy.datatypes.genetics.Rgenetics

linkage pedigree (ped,map) Rgenetics data collections

file_ext = 'lped'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for all transformed versions of this genetic dataset, defaults to 'RgeneticsData'

class galaxy.datatypes.genetics.Pphe(**kwd)

Bases: galaxy.datatypes.genetics.Rgenetics

Plink phenotype file - header must have FID IID… Rgenetics data collections

file_ext = 'pphe'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for all transformed versions of this genetic dataset, defaults to 'RgeneticsData'

class galaxy.datatypes.genetics.Fphe(**kwd)

Bases: galaxy.datatypes.genetics.Rgenetics

fbat pedigree file - mad format with ! as first char on header row Rgenetics data collections

file_ext = 'fphe'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for all transformed versions of this genetic dataset, defaults to 'RgeneticsData'

class galaxy.datatypes.genetics.Phe(**kwd)

Bases: galaxy.datatypes.genetics.Rgenetics

Phenotype file

file_ext = 'phe'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for all transformed versions of this genetic dataset, defaults to 'RgeneticsData'

class galaxy.datatypes.genetics.Fped(**kwd)

Bases: galaxy.datatypes.genetics.Rgenetics

FBAT pedigree format - single file, map is header row of rs numbers. Strange. Rgenetics data collections

file_ext = 'fped'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for all transformed versions of this genetic dataset, defaults to 'RgeneticsData'

class galaxy.datatypes.genetics.Pbed(**kwd)

Bases: galaxy.datatypes.genetics.Rgenetics

Plink Binary compressed 2bit/geno Rgenetics data collections

file_ext = 'pbed'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for all transformed versions of this genetic dataset, defaults to 'RgeneticsData'

class galaxy.datatypes.genetics.ldIndep(**kwd)

Bases: galaxy.datatypes.genetics.Rgenetics

LD (a good measure of redundancy of information) depleted Plink Binary compressed 2bit/geno This is really a plink binary, but some tools work better with less redundancy so are constrained to these files

file_ext = 'ldreduced'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for all transformed versions of this genetic dataset, defaults to 'RgeneticsData'

class galaxy.datatypes.genetics.Eigenstratgeno(**kwd)

Bases: galaxy.datatypes.genetics.Rgenetics

Eigenstrat format - may be able to get rid of this if we move to shellfish Rgenetics data collections

file_ext = 'eigenstratgeno'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for all transformed versions of this genetic dataset, defaults to 'RgeneticsData'

class galaxy.datatypes.genetics.Eigenstratpca(**kwd)

Bases: galaxy.datatypes.genetics.Rgenetics

Eigenstrat PCA file for case control adjustment Rgenetics data collections

file_ext = 'eigenstratpca'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for all transformed versions of this genetic dataset, defaults to 'RgeneticsData'

class galaxy.datatypes.genetics.Snptest(**kwd)

Bases: galaxy.datatypes.genetics.Rgenetics

BioC snptest Rgenetics data collections

file_ext = 'snptest'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for all transformed versions of this genetic dataset, defaults to 'RgeneticsData'

class galaxy.datatypes.genetics.IdeasPre(**kwd)

Bases: galaxy.datatypes.text.Html

This datatype defines the input format required by IDEAS: https://academic.oup.com/nar/article/44/14/6721/2468150 The IDEAS preprocessor tool produces an output using this format. The extra_files_path of the primary input dataset contains the following files and directories. - chromosome_windows.txt (optional) - chromosomes.bed (optional) - IDEAS_input_config.txt - compressed archived tmp directory containing a number of compressed bed files.

composite_type = 'auto_primary_file'

allow_datatype_change = False

file_ext = 'ideaspre'

__init__(**kwd)

set_meta(dataset, **kwd)

generate_primary_file(dataset=None)

regenerate_primary_file(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): Base name for this dataset, defaults to 'IDEASData', chrom_bed (MetadataParameter): Bed file specifying window positions, defaults to 'None', chrom_windows (MetadataParameter): Chromosome window positions, defaults to 'None', input_config (MetadataParameter): IDEAS input config, defaults to 'None', tmp_archive (MetadataParameter): Compressed archive of compressed bed files, defaults to 'None'

class galaxy.datatypes.genetics.Pheno(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

base class for pheno files

file_ext = 'pheno'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.genetics.RexpBase(**kwd)

Bases: galaxy.datatypes.text.Html

base class for BioC data structures in Galaxy must be constructed with the pheno data in place since that goes into the metadata for each instance

file_ext = 'rexpbase'

html_table = None

composite_type = 'auto_primary_file'

allow_datatype_change = False

__init__(**kwd)

generate_primary_file(dataset=None)

This is called only at upload to write the html file cannot rename the datasets here - they come with the default unfortunately

get_mime()

Returns the mime type of the datatype

get_phecols(phenolist=[], maxConc=20)

sept 2009: cannot use whitespace to split - make a more complex structure here and adjust the methods that rely on this structure return interesting phenotype column names for an rexpression eset or affybatch to use in array subsetting and so on. Returns a data structure for a dynamic Galaxy select parameter. A column with only 1 value doesn’t change, so is not interesting for analysis. A column with a different value in every row is equivalent to a unique identifier so is also not interesting for anova or limma analysis - both these are removed after the concordance (count of unique terms) is constructed for each column. Then a complication - each remaining pair of columns is tested for redundancy - if two columns are always paired, then only one is needed :)

get_pheno(dataset)

expects a .pheno file in the extra_files_dir - ugh note that R is wierd and adds the row.name in the header so the columns are all wrong - unless you tell it not to. A file can be written as write.table(file=’foo.pheno’,pData(foo),sep=’ ‘,quote=F,row.names=F)

set_peek(dataset, **kwd)

expects a .pheno file in the extra_files_dir - ugh note that R is weird and does not include the row.name in the header. why?

get_peek(dataset)

expects a .pheno file in the extra_files_dir - ugh

get_file_peek(filename)

can’t really peek at a filename - need the extra_files_path and such?

regenerate_primary_file(dataset)

cannot do this until we are setting metadata

init_meta(dataset, copy_from=None)

set_meta(dataset, **kwd)

NOTE we apply the tabular machinary to the phenodata extracted from a BioC eSet or affybatch.

make_html_table(pp='nothing supplied from peek\n')

Create HTML table, used for displaying peek

display_peek(dataset)

Returns formatted html of peek

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_names (MetadataParameter): Column names, defaults to '[]', pheCols (MetadataParameter): Select list for potentially interesting variables, defaults to '[]', base_name (MetadataParameter): base name for all transformed versions of this expression dataset, defaults to 'rexpression', pheno_path (MetadataParameter): Path to phenotype data for this experiment, defaults to 'rexpression.pheno'

class galaxy.datatypes.genetics.Affybatch(**kwd)

Bases: galaxy.datatypes.genetics.RexpBase

derived class for BioC data structures in Galaxy

file_ext = 'affybatch'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_names (MetadataParameter): Column names, defaults to '[]', pheCols (MetadataParameter): Select list for potentially interesting variables, defaults to '[]', base_name (MetadataParameter): base name for all transformed versions of this expression dataset, defaults to 'rexpression', pheno_path (MetadataParameter): Path to phenotype data for this experiment, defaults to 'rexpression.pheno'

class galaxy.datatypes.genetics.Eset(**kwd)

Bases: galaxy.datatypes.genetics.RexpBase

derived class for BioC data structures in Galaxy

file_ext = 'eset'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_names (MetadataParameter): Column names, defaults to '[]', pheCols (MetadataParameter): Select list for potentially interesting variables, defaults to '[]', base_name (MetadataParameter): base name for all transformed versions of this expression dataset, defaults to 'rexpression', pheno_path (MetadataParameter): Path to phenotype data for this experiment, defaults to 'rexpression.pheno'

class galaxy.datatypes.genetics.MAlist(**kwd)

Bases: galaxy.datatypes.genetics.RexpBase

derived class for BioC data structures in Galaxy

file_ext = 'malist'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_names (MetadataParameter): Column names, defaults to '[]', pheCols (MetadataParameter): Select list for potentially interesting variables, defaults to '[]', base_name (MetadataParameter): base name for all transformed versions of this expression dataset, defaults to 'rexpression', pheno_path (MetadataParameter): Path to phenotype data for this experiment, defaults to 'rexpression.pheno'

class galaxy.datatypes.genetics.LinkageStudies(**kwd)

Bases: galaxy.datatypes.data.Text

superclass for classical linkage analysis suites

test_files = ['linkstudies.allegro_fparam', 'linkstudies.alohomora_gts', 'linkstudies.linkage_datain', 'linkstudies.linkage_map']

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.genetics.GenotypeMatrix(**kwd)

Bases: galaxy.datatypes.genetics.LinkageStudies

Sample matrix of genotypes - GTs as columns

file_ext = 'alohomora_gts'

__init__(**kwd)

header_check(fio)

sniff_prefix(file_prefix)

>>> classname = GenotypeMatrix
>>> from galaxy.datatypes.sniff import get_test_fname
>>> extn_true = classname().file_ext
>>> file_true = get_test_fname("linkstudies." + extn_true)
>>> classname().sniff(file_true)
True
>>> false_files = list(LinkageStudies.test_files)
>>> false_files.remove("linkstudies." + extn_true)
>>> result_true = []
>>> for fname in false_files:
...     file_false = get_test_fname(fname)
...     res = classname().sniff(file_false)
...     if res:
...         result_true.append(fname)
>>>
>>> result_true
[]

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.genetics.MarkerMap(**kwd)

Bases: galaxy.datatypes.genetics.LinkageStudies

Map of genetic markers including physical and genetic distance Common input format for linkage programs

chrom, genetic pos, markername, physical pos, Nr

file_ext = 'linkage_map'

header_check(fio)

sniff_prefix(file_prefix)

>>> classname = MarkerMap
>>> from galaxy.datatypes.sniff import get_test_fname
>>> extn_true = classname().file_ext
>>> file_true = get_test_fname("linkstudies." + extn_true)
>>> classname().sniff(file_true)
True
>>> false_files = list(LinkageStudies.test_files)
>>> false_files.remove("linkstudies." + extn_true)
>>> result_true = []
>>> for fname in false_files:
...     file_false = get_test_fname(fname)
...     res = classname().sniff(file_false)
...     if res:
...         result_true.append(fname)
>>>
>>> result_true
[]

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.genetics.DataIn(**kwd)

Bases: galaxy.datatypes.genetics.LinkageStudies

Common linkage input file for intermarker distances and recombination rates

file_ext = 'linkage_datain'

__init__(**kwd)

sniff_prefix(file_prefix)

>>> classname = DataIn
>>> from galaxy.datatypes.sniff import get_test_fname
>>> extn_true = classname().file_ext
>>> file_true = get_test_fname("linkstudies." + extn_true)
>>> classname().sniff(file_true)
True
>>> false_files = list(LinkageStudies.test_files)
>>> false_files.remove("linkstudies." + extn_true)
>>> result_true = []
>>> for fname in false_files:
...     file_false = get_test_fname(fname)
...     res = classname().sniff(file_false)
...     if res:
...         result_true.append(fname)
>>>
>>> result_true
[]

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.genetics.AllegroLOD(**kwd)

Bases: galaxy.datatypes.genetics.LinkageStudies

Allegro output format for LOD scores

file_ext = 'allegro_fparam'

header_check(fio)

sniff_prefix(file_prefix)

>>> classname = AllegroLOD
>>> from galaxy.datatypes.sniff import get_test_fname
>>> extn_true = classname().file_ext
>>> file_true = get_test_fname("linkstudies." + extn_true)
>>> classname().sniff(file_true)
True
>>> false_files = list(LinkageStudies.test_files)
>>> false_files.remove("linkstudies." + extn_true)
>>> result_true = []
>>> for fname in false_files:
...     file_false = get_test_fname(fname)
...     res = classname().sniff(file_false)
...     if res:
...         result_true.append(fname)
>>>
>>> result_true
[]

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

galaxy.datatypes.graph module

Graph content classes.

class galaxy.datatypes.graph.Xgmml(**kwd)

Bases: galaxy.datatypes.xml.GenericXml

XGMML graph format (http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats).

file_ext = 'xgmml'

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

sniff(filename)

Returns false and the user must manually set.

static merge(split_files, output_file)

Merging multiple XML files is non-trivial and must be done in subclasses.

node_edge_dataprovider(*args, **kwargs)

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'node-edge': <function node_edge_dataprovider at 0x7fbb266f9848>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>, 'xml': <function xml_dataprovider at 0x7fbb327fc2a8>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.graph.Sif(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

SIF graph format (http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats).

First column: node id Second column: relationship type Third to Nth column: target ids for link

file_ext = 'sif'

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

sniff(filename)

Returns false and the user must manually set.

static merge(split_files, output_file)

node_edge_dataprovider(*args, **kwargs)

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'column': <function column_dataprovider at 0x7fbb50a72320>, 'dataset-column': <function dataset_column_dataprovider at 0x7fbb50a72488>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7fbb50a72758>, 'dict': <function dict_dataprovider at 0x7fbb50a725f0>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'node-edge': <function node_edge_dataprovider at 0x7fbb2597d578>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.graph.XGMMLGraphDataProvider(source, selector=None, max_depth=None, **kwargs)

Bases: galaxy.datatypes.dataproviders.hierarchy.XMLDataProvider

Provide two lists: nodes, edges:

'nodes': contains objects of the form:
    { 'id' : <some string id>, 'data': <any extra data> }
'edges': contains objects of the form:
    { 'source' : <an index into nodes>, 'target': <an index into nodes>, 'data': <any extra data> }

settings = {'limit': 'int', 'max_depth': 'int', 'offset': 'int', 'selector': 'str'}

class galaxy.datatypes.graph.SIFGraphDataProvider(source, indeces=None, column_count=None, column_types=None, parsers=None, parse_columns=True, deliminator='t', filters=None, **kwargs)

Bases: galaxy.datatypes.dataproviders.column.ColumnarDataProvider

Provide two lists: nodes, edges:

'nodes': contains objects of the form:
    { 'id' : <some string id>, 'data': <any extra data> }
'edges': contains objects of the form:
    { 'source' : <an index into nodes>, 'target': <an index into nodes>, 'data': <any extra data> }

settings = {'column_count': 'int', 'column_types': 'list:str', 'comment_char': 'str', 'deliminator': 'str', 'filters': 'list:str', 'indeces': 'list:int', 'invert': 'bool', 'limit': 'int', 'offset': 'int', 'parse_columns': 'bool', 'provide_blank': 'bool', 'regex_list': 'list:escaped', 'strip_lines': 'bool', 'strip_newlines': 'bool'}

galaxy.datatypes.images module

Image classes

class galaxy.datatypes.images.Image(**kwd)

Bases: galaxy.datatypes.data.Data

Class describing an image

edam_data = 'data_2968'

edam_format = 'format_3547'

file_ext = ''

__init__(**kwd)

set_peek(dataset, is_multi_byte=False)

sniff(filename)

Determine if the file is in this format

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Jpg(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3579'

file_ext = 'jpg'

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Png(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3603'

file_ext = 'png'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Tiff(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3591'

file_ext = 'tiff'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Hamamatsu(**kwd)

Bases: galaxy.datatypes.images.Image

file_ext = 'vms'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Mirax(**kwd)

Bases: galaxy.datatypes.images.Image

file_ext = 'mrxs'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Sakura(**kwd)

Bases: galaxy.datatypes.images.Image

file_ext = 'svslide'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Nrrd(**kwd)

Bases: galaxy.datatypes.images.Image

file_ext = 'nrrd'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Bmp(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3592'

file_ext = 'bmp'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Gif(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3467'

file_ext = 'gif'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Im(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3593'

file_ext = 'im'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Pcd(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3594'

file_ext = 'pcd'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Pcx(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3595'

file_ext = 'pcx'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Ppm(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3596'

file_ext = 'ppm'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Psd(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3597'

file_ext = 'psd'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Xbm(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3598'

file_ext = 'xbm'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Xpm(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3599'

file_ext = 'xpm'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Rgb(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3600'

file_ext = 'rgb'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Pbm(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3601'

file_ext = 'pbm'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Pgm(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3602'

file_ext = 'pgm'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Eps(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3466'

file_ext = 'eps'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Rast(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3605'

file_ext = 'rast'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Pdf(**kwd)

Bases: galaxy.datatypes.images.Image

edam_format = 'format_3508'

file_ext = 'pdf'

sniff(filename)

Determine if the file is in pdf format.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

galaxy.datatypes.images.create_applet_tag_peek(class_name, archive, params)

class galaxy.datatypes.images.Gmaj(**kwd)

Bases: galaxy.datatypes.data.Data

Class describing a GMAJ Applet

edam_format = 'format_3547'

file_ext = 'gmaj.zip'

copy_safe_peek = False

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

get_mime()

Returns the mime type of the datatype

sniff(filename)

NOTE: the sniff.convert_newlines() call in the upload utility will keep Gmaj data types from being correctly sniffed, but the files can be uploaded (they’ll be sniffed as ‘txt’). This sniff function is here to provide an example of a sniffer for a zip file.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.images.Html(**kwd)

Bases: galaxy.datatypes.text.Html

Deprecated class. This class should not be used anymore, but the galaxy.datatypes.text:Html one. This is for backwards compatibilities only.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.images.Laj(**kwd)

Bases: galaxy.datatypes.data.Text

Class describing a LAJ Applet

file_ext = 'laj'

copy_safe_peek = False

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

galaxy.datatypes.interval module

Interval datatypes

class galaxy.datatypes.interval.Interval(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

Tab delimited data containing interval information

edam_data = 'data_3002'

edam_format = 'format_3475'

file_ext = 'interval'

line_class = 'region'

track_type = 'FeatureTrack'

data_sources = {'data': 'tabix', 'index': 'bigwig'}

Add metadata elements

__init__(**kwd)

Initialize interval datatype, by adding UCSC display apps

init_meta(dataset, copy_from=None)

set_meta(dataset, overwrite=True, first_line_is_header=False, **kwd)

Tries to guess from the line the location number of the column for the chromosome, region start-end and strand

displayable(dataset)

get_estimated_display_viewport(dataset, chrom_col=None, start_col=None, end_col=None)

Return a chrom, start, stop tuple for viewing a file.

as_ucsc_display_file(dataset, **kwd)

Returns file contents with only the bed data

display_peek(dataset)

Returns formated html of peek

ucsc_links(dataset, type, app, base_url)

Generate links to UCSC genome browser sites based on the dbkey and content of dataset.

validate(dataset)

Validate an interval file using the bx GenomicIntervalReader

repair_methods(dataset)

Return options for removing errors along with a description

sniff_prefix(file_prefix)

Checks for ‘intervalness’

This format is mostly used by galaxy itself. Valid interval files should include a valid header comment, but this seems to be loosely regulated.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'test_space.txt' )
>>> Interval().sniff( fname )
False
>>> fname = get_test_fname( 'interval.interval' )
>>> Interval().sniff( fname )
True

get_track_resolution(dataset, start, end)

genomic_region_dataprovider(*args, **kwargs)

genomic_region_dict_dataprovider(*args, **kwargs)

interval_dataprovider(*args, **kwargs)

interval_dict_dataprovider(*args, **kwargs)

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'column': <function column_dataprovider at 0x7fbb50a72320>, 'dataset-column': <function dataset_column_dataprovider at 0x7fbb50a72488>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7fbb50a72758>, 'dict': <function dict_dataprovider at 0x7fbb50a725f0>, 'genomic-region': <function genomic_region_dataprovider at 0x7fbb50937500>, 'genomic-region-dict': <function genomic_region_dict_dataprovider at 0x7fbb50937668>, 'interval': <function interval_dataprovider at 0x7fbb509377d0>, 'interval-dict': <function interval_dict_dataprovider at 0x7fbb50937938>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '3', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', chromCol (ColumnParameter): Chrom column, defaults to '1', startCol (ColumnParameter): Start column, defaults to '2', endCol (ColumnParameter): End column, defaults to '3', strandCol (ColumnParameter): Strand column (click box & select), defaults to 'None', nameCol (ColumnParameter): Name/Identifier column (click box & select), defaults to 'None'

sniff(filename)

class galaxy.datatypes.interval.BedGraph(**kwd)

Bases: galaxy.datatypes.interval.Interval

Tab delimited chrom/start/end/datavalue dataset

edam_format = 'format_3583'

file_ext = 'bedgraph'

track_type = 'LineTrack'

data_sources = {'data': 'bigwig', 'index': 'bigwig'}

as_ucsc_display_file(dataset, **kwd)

Returns file contents as is with no modifications. TODO: this is a functional stub and will need to be enhanced moving forward to provide additional support for bedgraph.

get_estimated_display_viewport(dataset, chrom_col=0, start_col=1, end_col=2)

Set viewport based on dataset’s first 100 lines.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '3', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', chromCol (ColumnParameter): Chrom column, defaults to '1', startCol (ColumnParameter): Start column, defaults to '2', endCol (ColumnParameter): End column, defaults to '3', strandCol (ColumnParameter): Strand column (click box & select), defaults to 'None', nameCol (ColumnParameter): Name/Identifier column (click box & select), defaults to 'None'

class galaxy.datatypes.interval.Bed(**kwd)

Bases: galaxy.datatypes.interval.Interval

Tab delimited data in BED format

edam_format = 'format_3003'

file_ext = 'bed'

data_sources = {'data': 'tabix', 'feature_search': 'fli', 'index': 'bigwig'}

track_type = 'FeatureTrack'

column_names = ['Chrom', 'Start', 'End', 'Name', 'Score', 'Strand', 'ThickStart', 'ThickEnd', 'ItemRGB', 'BlockCount', 'BlockSizes', 'BlockStarts']

Add metadata elements

set_meta(dataset, overwrite=True, **kwd)

Sets the metadata information for datasets previously determined to be in bed format.

as_ucsc_display_file(dataset, **kwd)

Returns file contents with only the bed data. If bed 6+, treat as interval.

sniff_prefix(file_prefix)

Checks for ‘bedness’

BED lines have three required fields and nine additional optional fields. The number of fields per line must be consistent throughout any single set of data in an annotation track. The order of the optional fields is binding: lower-numbered fields must always be populated if higher-numbered fields are used. The data type of all 12 columns is: 1-str, 2-int, 3-int, 4-str, 5-int, 6-str, 7-int, 8-int, 9-int or list, 10-int, 11-list, 12-list

For complete details see http://genome.ucsc.edu/FAQ/FAQformat#format1

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'test_tab.bed' )
>>> Bed().sniff( fname )
True
>>> fname = get_test_fname( 'interval1.bed' )
>>> Bed().sniff( fname )
True
>>> fname = get_test_fname( 'complete.bed' )
>>> Bed().sniff( fname )
True

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '3', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', chromCol (ColumnParameter): Chrom column, defaults to '1', startCol (ColumnParameter): Start column, defaults to '2', endCol (ColumnParameter): End column, defaults to '3', strandCol (ColumnParameter): Strand column (click box & select), defaults to 'None', nameCol (ColumnParameter): Name/Identifier column (click box & select), defaults to 'None', viz_filter_cols (ColumnParameter): Score column for visualization, defaults to '[4]'

class galaxy.datatypes.interval.ProBed(**kwd)

Bases: galaxy.datatypes.interval.Bed

Tab delimited data in proBED format - adaptation of BED for proteomics data.

edam_format = 'format_3827'

file_ext = 'probed'

column_names = ['Chrom', 'Start', 'End', 'Name', 'Score', 'Strand', 'ThickStart', 'ThickEnd', 'ItemRGB', 'BlockCount', 'BlockSizes', 'BlockStarts', 'ProteinAccession', 'PeptideSequence', 'Uniqueness', 'GenomeReferenceVersion', 'PsmScore', 'Fdr', 'Modifications', 'Charge', 'ExpMassToCharge', 'CalcMassToCharge', 'PsmRank', 'DatasetID', 'Uri']

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '3', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', chromCol (ColumnParameter): Chrom column, defaults to '1', startCol (ColumnParameter): Start column, defaults to '2', endCol (ColumnParameter): End column, defaults to '3', strandCol (ColumnParameter): Strand column (click box & select), defaults to 'None', nameCol (ColumnParameter): Name/Identifier column (click box & select), defaults to 'None', viz_filter_cols (ColumnParameter): Score column for visualization, defaults to '[4]'

class galaxy.datatypes.interval.BedStrict(**kwd)

Bases: galaxy.datatypes.interval.Bed

Tab delimited data in strict BED format - no non-standard columns allowed

edam_format = 'format_3584'

file_ext = 'bedstrict'

allow_datatype_change = False

__init__(**kwd)

set_meta(dataset, overwrite=True, **kwd)

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '3', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', chromCol (MetadataParameter): Chrom column, defaults to '1', startCol (MetadataParameter): Start column, defaults to '2', endCol (MetadataParameter): End column, defaults to '3', strandCol (MetadataParameter): Strand column (click box & select), defaults to 'None', nameCol (MetadataParameter): Name/Identifier column (click box & select), defaults to 'None', viz_filter_cols (ColumnParameter): Score column for visualization, defaults to '[4]'

class galaxy.datatypes.interval.Bed6(**kwd)

Bases: galaxy.datatypes.interval.BedStrict

Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 6

edam_format = 'format_3585'

file_ext = 'bed6'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '3', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', chromCol (MetadataParameter): Chrom column, defaults to '1', startCol (MetadataParameter): Start column, defaults to '2', endCol (MetadataParameter): End column, defaults to '3', strandCol (MetadataParameter): Strand column (click box & select), defaults to 'None', nameCol (MetadataParameter): Name/Identifier column (click box & select), defaults to 'None', viz_filter_cols (ColumnParameter): Score column for visualization, defaults to '[4]'

class galaxy.datatypes.interval.Bed12(**kwd)

Bases: galaxy.datatypes.interval.BedStrict

Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 12

edam_format = 'format_3586'

file_ext = 'bed12'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '3', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', chromCol (MetadataParameter): Chrom column, defaults to '1', startCol (MetadataParameter): Start column, defaults to '2', endCol (MetadataParameter): End column, defaults to '3', strandCol (MetadataParameter): Strand column (click box & select), defaults to 'None', nameCol (MetadataParameter): Name/Identifier column (click box & select), defaults to 'None', viz_filter_cols (ColumnParameter): Score column for visualization, defaults to '[4]'

class galaxy.datatypes.interval.Gff(**kwd)

Bases: galaxy.datatypes.tabular.Tabular, galaxy.datatypes.interval._RemoteCallMixin

Tab delimited data in Gff format

edam_data = 'data_1255'

edam_format = 'format_2305'

file_ext = 'gff'

valid_gff_frame = ['.', '0', '1', '2']

column_names = ['Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group']

data_sources = {'data': 'interval_index', 'feature_search': 'fli', 'index': 'bigwig'}

track_type = 'FeatureTrack'

Add metadata elements

__init__(**kwd)

Initialize datatype, by adding GBrowse display app

set_attribute_metadata(dataset)

Sets metadata elements for dataset’s attributes.

set_meta(dataset, overwrite=True, **kwd)

display_peek(dataset)

Returns formated html of peek

get_estimated_display_viewport(dataset)

Return a chrom, start, stop tuple for viewing a file. There are slight differences between gff 2 and gff 3 formats. This function should correctly handle both…

ucsc_links(dataset, type, app, base_url)

gbrowse_links(dataset, type, app, base_url)

sniff_prefix(file_prefix)

Determines whether the file is in gff format

GFF lines have nine required fields that must be tab-separated.

For complete details see http://genome.ucsc.edu/FAQ/FAQformat#format3

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('gff_version_3.gff')
>>> Gff().sniff( fname )
False
>>> fname = get_test_fname('test.gff')
>>> Gff().sniff( fname )
True

genomic_region_dataprovider(*args, **kwargs)

genomic_region_dict_dataprovider(*args, **kwargs)

interval_dataprovider(*args, **kwargs)

interval_dict_dataprovider(*args, **kwargs)

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'column': <function column_dataprovider at 0x7fbb50a72320>, 'dataset-column': <function dataset_column_dataprovider at 0x7fbb50a72488>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7fbb50a72758>, 'dict': <function dict_dataprovider at 0x7fbb50a725f0>, 'genomic-region': <function genomic_region_dataprovider at 0x7fbb5093ede8>, 'genomic-region-dict': <function genomic_region_dict_dataprovider at 0x7fbb5093ef50>, 'interval': <function interval_dataprovider at 0x7fbb50949140>, 'interval-dict': <function interval_dict_dataprovider at 0x7fbb509492a8>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '9', column_types (ColumnTypesParameter): Column types, defaults to '['str', 'str', 'str', 'int', 'int', 'int', 'str', 'str', 'str']', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', attributes (MetadataParameter): Number of attributes, defaults to '0', attribute_types (DictParameter): Attribute types, defaults to '{}'

sniff(filename)

class galaxy.datatypes.interval.Gff3(**kwd)

Bases: galaxy.datatypes.interval.Gff

Tab delimited data in Gff3 format

edam_format = 'format_1975'

file_ext = 'gff3'

valid_gff3_strand = ['+', '-', '.', '?']

valid_gff3_phase = ['.', '0', '1', '2']

column_names = ['Seqid', 'Source', 'Type', 'Start', 'End', 'Score', 'Strand', 'Phase', 'Attributes']

track_type = 'FeatureTrack'

Add metadata elements

__init__(**kwd)

Initialize datatype, by adding GBrowse display app

set_meta(dataset, overwrite=True, **kwd)

sniff_prefix(file_prefix)

Determines whether the file is in GFF version 3 format

GFF 3 format:

1. adds a mechanism for representing more than one level of hierarchical grouping of features and subfeatures.
2. separates the ideas of group membership and feature name/id
3. constrains the feature type field to be taken from a controlled vocabulary.
4. allows a single feature, such as an exon, to belong to more than one group at a time.
5. provides an explicit convention for pairwise alignments
6. provides an explicit convention for features that occupy disjunct regions

The format consists of 9 columns, separated by tabs (NOT spaces).

Undefined fields are replaced with the “.” character, as described in the original GFF spec.

For complete details see http://song.sourceforge.net/gff3.shtml

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'test.gff' )
>>> Gff3().sniff( fname )
False
>>> fname = get_test_fname( 'test.gtf' )
>>> Gff3().sniff( fname )
False
>>> fname = get_test_fname('gff_version_3.gff')
>>> Gff3().sniff( fname )
True

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '9', column_types (ColumnTypesParameter): Column types, defaults to '['str', 'str', 'str', 'int', 'int', 'float', 'str', 'int', 'list']', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', attributes (MetadataParameter): Number of attributes, defaults to '0', attribute_types (DictParameter): Attribute types, defaults to '{}'

class galaxy.datatypes.interval.Gtf(**kwd)

Bases: galaxy.datatypes.interval.Gff

Tab delimited data in Gtf format

edam_format = 'format_2306'

file_ext = 'gtf'

column_names = ['Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Attributes']

track_type = 'FeatureTrack'

Add metadata elements

sniff_prefix(file_prefix)

Determines whether the file is in gtf format

GTF lines have nine required fields that must be tab-separated. The first eight GTF fields are the same as GFF. The group field has been expanded into a list of attributes. Each attribute consists of a type/value pair. Attributes must end in a semi-colon, and be separated from any following attribute by exactly one space. The attribute list must begin with the two mandatory attributes:

gene_id value - A globally unique identifier for the genomic source of the sequence. transcript_id value - A globally unique identifier for the predicted transcript.

For complete details see http://genome.ucsc.edu/FAQ/FAQformat#format4

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( '1.bed' )
>>> Gtf().sniff( fname )
False
>>> fname = get_test_fname( 'test.gff' )
>>> Gtf().sniff( fname )
False
>>> fname = get_test_fname( 'test.gtf' )
>>> Gtf().sniff( fname )
True

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '9', column_types (ColumnTypesParameter): Column types, defaults to '['str', 'str', 'str', 'int', 'int', 'float', 'str', 'int', 'list']', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', attributes (MetadataParameter): Number of attributes, defaults to '0', attribute_types (DictParameter): Attribute types, defaults to '{}'

class galaxy.datatypes.interval.Wiggle(**kwd)

Bases: galaxy.datatypes.tabular.Tabular, galaxy.datatypes.interval._RemoteCallMixin

Tab delimited data in wiggle format

edam_format = 'format_3005'

file_ext = 'wig'

track_type = 'LineTrack'

data_sources = {'data': 'bigwig', 'index': 'bigwig'}

__init__(**kwd)

get_estimated_display_viewport(dataset)

Return a chrom, start, stop tuple for viewing a file.

gbrowse_links(dataset, type, app, base_url)

ucsc_links(dataset, type, app, base_url)

display_peek(dataset)

Returns formated html of peek

set_meta(dataset, overwrite=True, **kwd)

sniff_prefix(file_prefix)

Determines wether the file is in wiggle format

The .wig format is line-oriented. Wiggle data is preceeded by a track definition line, which adds a number of options for controlling the default display of this track. Following the track definition line is the track data, which can be entered in several different formats.

The track definition line begins with the word ‘track’ followed by the track type. The track type with version is REQUIRED, and it currently must be wiggle_0. For example, track type=wiggle_0…

For complete details see http://genome.ucsc.edu/goldenPath/help/wiggle.html

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'interval1.bed' )
>>> Wiggle().sniff( fname )
False
>>> fname = get_test_fname( 'wiggle.wig' )
>>> Wiggle().sniff( fname )
True

get_track_resolution(dataset, start, end)

wiggle_dataprovider(*args, **kwargs)

wiggle_dict_dataprovider(*args, **kwargs)

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'column': <function column_dataprovider at 0x7fbb50a72320>, 'dataset-column': <function dataset_column_dataprovider at 0x7fbb50a72488>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7fbb50a72758>, 'dict': <function dict_dataprovider at 0x7fbb50a725f0>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>, 'wiggle': <function wiggle_dataprovider at 0x7fbb50949f50>, 'wiggle-dict': <function wiggle_dict_dataprovider at 0x7fbb5094e140>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '3', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

sniff(filename)

class galaxy.datatypes.interval.CustomTrack(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

UCSC CustomTrack

edam_format = 'format_3588'

file_ext = 'customtrack'

__init__(**kwd)

Initialize interval datatype, by adding UCSC display app

set_meta(dataset, overwrite=True, **kwd)

display_peek(dataset)

Returns formated html of peek

get_estimated_display_viewport(dataset, chrom_col=None, start_col=None, end_col=None)

Return a chrom, start, stop tuple for viewing a file.

ucsc_links(dataset, type, app, base_url)

sniff_prefix(file_prefix)

Determines whether the file is in customtrack format.

CustomTrack files are built within Galaxy and are basically bed or interval files with the first line looking something like this.

track name=”User Track” description=”User Supplied Track (from Galaxy)” color=0,0,0 visibility=1

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'complete.bed' )
>>> CustomTrack().sniff( fname )
False
>>> fname = get_test_fname( 'ucsc.customtrack' )
>>> CustomTrack().sniff( fname )
True

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

sniff(filename)

class galaxy.datatypes.interval.ENCODEPeak(**kwd)

Bases: galaxy.datatypes.interval.Interval

Human ENCODE peak format. There are both broad and narrow peak formats. Formats are very similar; narrow peak has an additional column, though.

Broad peak ( http://genome.ucsc.edu/FAQ/FAQformat#format13 ): This format is used to provide called regions of signal enrichment based on pooled, normalized (interpreted) data. It is a BED 6+3 format.

Narrow peak http://genome.ucsc.edu/FAQ/FAQformat#format12 and : This format is used to provide called peaks of signal enrichment based on pooled, normalized (interpreted) data. It is a BED6+4 format.

edam_format = 'format_3612'

file_ext = 'encodepeak'

column_names = ['Chrom', 'Start', 'End', 'Name', 'Score', 'Strand', 'SignalValue', 'pValue', 'qValue', 'Peak']

data_sources = {'data': 'tabix', 'index': 'bigwig'}

Add metadata elements

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '3', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', chromCol (ColumnParameter): Chrom column, defaults to '1', startCol (ColumnParameter): Start column, defaults to '2', endCol (ColumnParameter): End column, defaults to '3', strandCol (ColumnParameter): Strand column (click box & select), defaults to 'None', nameCol (ColumnParameter): Name/Identifier column (click box & select), defaults to 'None'

class galaxy.datatypes.interval.ChromatinInteractions(**kwd)

Bases: galaxy.datatypes.interval.Interval

Chromatin interactions obtained from 3C/5C/Hi-C experiments.

file_ext = 'chrint'

track_type = 'DiagonalHeatmapTrack'

data_sources = {'data': 'tabix', 'index': 'bigwig'}

column_names = ['Chrom1', 'Start1', 'End1', 'Chrom2', 'Start2', 'End2', 'Value']

Add metadata elements

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '7', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', chromCol (ColumnParameter): Chrom column, defaults to '1', startCol (ColumnParameter): Start column, defaults to '2', endCol (ColumnParameter): End column, defaults to '3', strandCol (ColumnParameter): Strand column (click box & select), defaults to 'None', nameCol (ColumnParameter): Name/Identifier column (click box & select), defaults to 'None', chrom1Col (ColumnParameter): Chrom1 column, defaults to '1', start1Col (ColumnParameter): Start1 column, defaults to '2', end1Col (ColumnParameter): End1 column, defaults to '3', chrom2Col (ColumnParameter): Chrom2 column, defaults to '4', start2Col (ColumnParameter): Start2 column, defaults to '5', end2Col (ColumnParameter): End2 column, defaults to '6', valueCol (ColumnParameter): Value column, defaults to '7'

sniff(filename)

class galaxy.datatypes.interval.ScIdx(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

ScIdx files are 1-based and consist of strand-specific coordinate counts. They always have 5 columns, and the first row is the column labels: ‘chrom’, ‘index’, ‘forward’, ‘reverse’, ‘value’. Each line following the first consists of data: chromosome name (type str), peak index (type int), Forward strand peak count (type int), Reverse strand peak count (type int) and value (type int). The value of the 5th ‘value’ column is the sum of the forward and reverse peak count values.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

sniff(filename)

file_ext = 'scidx'

__init__(**kwd)

Initialize scidx datatype.

sniff_prefix(file_prefix)

Checks for ‘scidx-ness.’

galaxy.datatypes.metadata module

Expose the model metadata module as a datatype module also, allowing it to live in galaxy.model means the model module doesn’t have any dependencies on th datatypes module. This module will need to remain here for datatypes living in the tool shed so we might as well keep and use this interface from the datatypes module.

class galaxy.datatypes.metadata.Statement(target)

Bases: object

This class inserts its target into a list in the surrounding class. the data.Data class has a metaclass which executes these statements. This is how we shove the metadata element spec into the class.

__init__(target)

classmethod process(element)

class galaxy.datatypes.metadata.MetadataCollection(parent)

Bases: object

MetadataCollection is not a collection at all, but rather a proxy to the real metadata which is stored as a Dictionary. This class handles processing the metadata elements when they are set and retrieved, returning default values in cases when metadata is not set.

__init__(parent)

get_parent()

set_parent(parent)

parent

spec

get(key, default=None)

items()

remove_key(name)

element_is_set(name)

get_metadata_parameter(name, **kwd)

make_dict_copy(to_copy)

Makes a deep copy of input iterable to_copy according to self.spec

requires_dataset_id

from_JSON_dict(filename=None, path_rewriter=None, json_dict=None)

to_JSON_dict(filename=None)

class galaxy.datatypes.metadata.MetadataSpecCollection(dict=None)

Bases: galaxy.util.odict.odict

A simple extension of dict which allows cleaner access to items and allows the values to be iterated over directly as if it were a list. append() is also implemented for simplicity and does not “append”.

__init__(dict=None)

append(item)

iter()

class galaxy.datatypes.metadata.MetadataParameter(spec)

Bases: object

__init__(spec)

get_field(value=None, context=None, other_values=None, **kwd)

to_string(value)

to_safe_string(value)

make_copy(value, target_context=None, source_context=None)

classmethod marshal(value)

This method should/can be overridden to convert the incoming value to whatever type it is supposed to be.

validate(value)

Throw an exception if the value is invalid.

unwrap(form_value)

Turns a value into its storable form.

wrap(value, session)

Turns a value into its usable form.

from_external_value(value, parent)

Turns a value read from an external dict into its value to be pushed directly into the metadata dict.

to_external_value(value)

Turns a value read from a metadata into its value to be pushed directly into the external dict.

class galaxy.datatypes.metadata.MetadataElementSpec(datatype, name=None, desc=None, param=<class 'galaxy.model.metadata.MetadataParameter'>, default=None, no_value=None, visible=True, set_in_upload=False, **kwargs)

Bases: object

Defines a metadata element and adds it to the metadata_spec (which is a MetadataSpecCollection) of datatype.

__init__(datatype, name=None, desc=None, param=<class 'galaxy.model.metadata.MetadataParameter'>, default=None, no_value=None, visible=True, set_in_upload=False, **kwargs)

get(name, default=None)

wrap(value, session)

Turns a stored value into its usable form.

unwrap(value)

Turns an incoming value into its storable form.

class galaxy.datatypes.metadata.SelectParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

__init__(spec)

to_string(value)

get_field(value=None, context=None, other_values=None, values=None, **kwd)

wrap(value, session)

classmethod marshal(value)

class galaxy.datatypes.metadata.DBKeyParameter(spec)

Bases: galaxy.model.metadata.SelectParameter

get_field(value=None, context=None, other_values=None, values=None, **kwd)

class galaxy.datatypes.metadata.RangeParameter(spec)

Bases: galaxy.model.metadata.SelectParameter

__init__(spec)

get_field(value=None, context=None, other_values=None, values=None, **kwd)

classmethod marshal(value)

class galaxy.datatypes.metadata.ColumnParameter(spec)

Bases: galaxy.model.metadata.RangeParameter

get_field(value=None, context=None, other_values=None, values=None, **kwd)

class galaxy.datatypes.metadata.ColumnTypesParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

class galaxy.datatypes.metadata.ListParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

class galaxy.datatypes.metadata.DictParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

to_safe_string(value)

class galaxy.datatypes.metadata.PythonObjectParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

get_field(value=None, context=None, other_values=None, **kwd)

classmethod marshal(value)

class galaxy.datatypes.metadata.FileParameter(spec)

Bases: galaxy.model.metadata.MetadataParameter

to_string(value)

to_safe_string(value)

get_field(value=None, context=None, other_values=None, **kwd)

wrap(value, session)

make_copy(value, target_context, source_context)

classmethod marshal(value)

from_external_value(value, parent, path_rewriter=None)

Turns a value read from a external dict into its value to be pushed directly into the metadata dict.

to_external_value(value)

Turns a value read from a metadata into its value to be pushed directly into the external dict.

new_file(dataset=None, **kwds)

class galaxy.datatypes.metadata.MetadataTempFile(**kwds)

Bases: object

tmp_dir = 'database/tmp'

__init__(**kwds)

file_name

to_JSON()

classmethod from_JSON(json_dict)

classmethod is_JSONified_value(value)

classmethod cleanup_from_JSON_dict_filename(filename)

class galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper(job)

Bases: object

Class with methods allowing set_meta() to be called externally to the Galaxy head. This class allows access to external metadata filenames for all outputs associated with a job. We will use JSON as the medium of exchange of information, except for the DatasetInstance object which will use pickle (in the future this could be JSONified as well)

__init__(job)

get_output_filenames_by_dataset(dataset, sa_session)

get_dataset_metadata_key(dataset)

invalidate_external_metadata(datasets, sa_session)

setup_external_metadata(datasets, sa_session, exec_dir=None, tmp_dir=None, dataset_files_path=None, output_fnames=None, config_root=None, config_file=None, datatypes_config=None, job_metadata=None, compute_tmp_dir=None, include_command=True, max_metadata_value_size=0, kwds=None)

external_metadata_set_successfully(dataset, sa_session)

cleanup_external_metadata(sa_session)

set_job_runner_external_pid(pid, sa_session)

galaxy.datatypes.molecules module

galaxy.datatypes.molecules.count_special_lines(word, filename, invert=False)

searching for special ‘words’ using the grep tool grep is used to speed up the searching and counting The number of hits is returned.

galaxy.datatypes.molecules.count_lines(filename, non_empty=False)

counting the number of lines from the ‘filename’ file

class galaxy.datatypes.molecules.GenericMolFile(**kwd)

Bases: galaxy.datatypes.data.Text

Abstract class for most of the molecule files.

set_peek(dataset, is_multi_byte=False)

get_mime()

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', number_of_molecules (MetadataParameter): Number of molecules, defaults to '0'

class galaxy.datatypes.molecules.MOL(**kwd)

Bases: galaxy.datatypes.molecules.GenericMolFile

file_ext = 'mol'

set_meta(dataset, **kwd)

Set the number molecules, in the case of MOL its always one.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', number_of_molecules (MetadataParameter): Number of molecules, defaults to '0'

class galaxy.datatypes.molecules.SDF(**kwd)

Bases: galaxy.datatypes.molecules.GenericMolFile

file_ext = 'sdf'

sniff_prefix(file_prefix)

Try to guess if the file is a SDF2 file.

An SDfile (structure-data file) can contain multiple compounds.

Each compound starts with a block in V2000 or V3000 molfile format, which ends with a line equal to ‘M END’. This is followed by a non-structural data block, which ends with a line equal to ‘$$$$’.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('drugbank_drugs.sdf')
>>> SDF().sniff(fname)
True
>>> fname = get_test_fname('github88.v3k.sdf')
>>> SDF().sniff(fname)
True
>>> fname = get_test_fname('chebi_57262.v3k.mol')
>>> SDF().sniff(fname)
False

set_meta(dataset, **kwd)

Set the number of molecules in dataset.

classmethod split(input_datasets, subdir_generator_function, split_params)

Split the input files by molecule records.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', number_of_molecules (MetadataParameter): Number of molecules, defaults to '0'

sniff(filename)

class galaxy.datatypes.molecules.MOL2(**kwd)

Bases: galaxy.datatypes.molecules.GenericMolFile

file_ext = 'mol2'

sniff_prefix(file_prefix)

Try to guess if the file is a MOL2 file.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('drugbank_drugs.mol2')
>>> MOL2().sniff(fname)
True
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> MOL2().sniff(fname)
False

set_meta(dataset, **kwd)

Set the number of lines of data in dataset.

classmethod split(input_datasets, subdir_generator_function, split_params)

Split the input files by molecule records.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', number_of_molecules (MetadataParameter): Number of molecules, defaults to '0'

sniff(filename)

class galaxy.datatypes.molecules.FPS(**kwd)

Bases: galaxy.datatypes.molecules.GenericMolFile

chemfp fingerprint file: http://code.google.com/p/chem-fingerprints/wiki/FPS

file_ext = 'fps'

sniff_prefix(file_prefix)

Try to guess if the file is a FPS file.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('q.fps')
>>> FPS().sniff(fname)
True
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> FPS().sniff(fname)
False

set_meta(dataset, **kwd)

Set the number of lines of data in dataset.

classmethod split(input_datasets, subdir_generator_function, split_params)

Split the input files by fingerprint records.

static merge(split_files, output_file)

Merging fps files requires merging the header manually. We take the header from the first file.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', number_of_molecules (MetadataParameter): Number of molecules, defaults to '0'

sniff(filename)

class galaxy.datatypes.molecules.OBFS(**kwd)

Bases: galaxy.datatypes.binary.Binary

OpenBabel Fastsearch format (fs).

file_ext = 'obfs'

composite_type = 'basic'

allow_datatype_change = False

__init__(**kwd)

A Fastsearch Index consists of a binary file with the fingerprints and a pointer the actual molecule file.

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text.

display_peek(dataset)

Create HTML content, used for displaying peek.

get_mime()

Returns the mime type of the datatype (pretend it is text for peek)

merge(split_files, output_file, extra_merge_args)

Merging Fastsearch indices is not supported.

split(input_datasets, subdir_generator_function, split_params)

Splitting Fastsearch indices is not supported.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', base_name (MetadataParameter): base_name, defaults to 'OpenBabel Fastsearch Index'

class galaxy.datatypes.molecules.DRF(**kwd)

Bases: galaxy.datatypes.molecules.GenericMolFile

file_ext = 'drf'

set_meta(dataset, **kwd)

Set the number of lines of data in dataset.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', number_of_molecules (MetadataParameter): Number of molecules, defaults to '0'

class galaxy.datatypes.molecules.PHAR(**kwd)

Bases: galaxy.datatypes.molecules.GenericMolFile

Pharmacophore database format from silicos-it.

file_ext = 'phar'

set_peek(dataset, is_multi_byte=False)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', number_of_molecules (MetadataParameter): Number of molecules, defaults to '0'

class galaxy.datatypes.molecules.PDB(**kwd)

Bases: galaxy.datatypes.molecules.GenericMolFile

Protein Databank format. http://www.wwpdb.org/documentation/format33/v3.3.html

file_ext = 'pdb'

sniff_prefix(file_prefix)

Try to guess if the file is a PDB file.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('5e5z.pdb')
>>> PDB().sniff(fname)
True
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> PDB().sniff(fname)
False

set_peek(dataset, is_multi_byte=False)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', number_of_molecules (MetadataParameter): Number of molecules, defaults to '0'

sniff(filename)

class galaxy.datatypes.molecules.PDBQT(**kwd)

Bases: galaxy.datatypes.molecules.GenericMolFile

PDBQT Autodock and Autodock Vina format http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file

file_ext = 'pdbqt'

sniff_prefix(file_prefix)

Try to guess if the file is a PDBQT file.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('NuBBE_1_obabel_3D.pdbqt')
>>> PDBQT().sniff(fname)
True
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> PDBQT().sniff(fname)
False

set_peek(dataset, is_multi_byte=False)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', number_of_molecules (MetadataParameter): Number of molecules, defaults to '0'

sniff(filename)

class galaxy.datatypes.molecules.grd(**kwd)

Bases: galaxy.datatypes.data.Text

file_ext = 'grd'

set_peek(dataset, is_multi_byte=False)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.molecules.grdtgz(**kwd)

Bases: galaxy.datatypes.binary.Binary

file_ext = 'grd.tgz'

set_peek(dataset, is_multi_byte=False)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.molecules.InChI(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'inchi'

column_names = ['InChI']

set_meta(dataset, **kwd)

Set the number of lines of data in dataset.

set_peek(dataset, is_multi_byte=False)

sniff_prefix(file_prefix)

Try to guess if the file is a InChI file.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('drugbank_drugs.inchi')
>>> InChI().sniff(fname)
True
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> InChI().sniff(fname)
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '2', column_types (ColumnTypesParameter): Column types, defaults to '['str']', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', number_of_molecules (MetadataParameter): Number of molecules, defaults to '0'

sniff(filename)

class galaxy.datatypes.molecules.SMILES(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'smi'

column_names = ['SMILES', 'TITLE']

set_meta(dataset, **kwd)

Set the number of lines of data in dataset.

set_peek(dataset, is_multi_byte=False)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '2', column_types (ColumnTypesParameter): Column types, defaults to '['str', 'str']', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', number_of_molecules (MetadataParameter): Number of molecules, defaults to '0'

class galaxy.datatypes.molecules.CML(**kwd)

Bases: galaxy.datatypes.xml.GenericXml

Chemical Markup Language http://cml.sourceforge.net/

file_ext = 'cml'

set_meta(dataset, **kwd)

Set the number of lines of data in dataset.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', number_of_molecules (MetadataParameter): Number of molecules, defaults to '0'

set_peek(dataset, is_multi_byte=False)

sniff(filename)

sniff_prefix(file_prefix)

Try to guess if the file is a CML file.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('interval.interval')
>>> CML().sniff(fname)
False
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> CML().sniff(fname)
True

classmethod split(input_datasets, subdir_generator_function, split_params)

Split the input files by molecule records.

static merge(split_files, output_file)

Merging CML files.

galaxy.datatypes.mothur module

Mothur Metagenomics Datatypes

class galaxy.datatypes.mothur.Otu(**kwd)

Bases: galaxy.datatypes.data.Text

file_ext = 'mothur.otu'

__init__(**kwd)

set_meta(dataset, overwrite=True, **kwd)

Set metadata for Otu files.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> from galaxy.util.bunch import Bunch
>>> dataset = Bunch()
>>> dataset.metadata = Bunch
>>> otu = Otu()
>>> dataset.file_name = get_test_fname( 'mothur_datatypetest_true.mothur.otu' )
>>> dataset.has_data = lambda: True
>>> otu.set_meta(dataset)
>>> dataset.metadata.columns
100
>>> len(dataset.metadata.labels) == 37
True
>>> len(dataset.metadata.otulabels) == 98
True

sniff_prefix(file_prefix)

Determines whether the file is otu (operational taxonomic unit) format

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.otu' )
>>> Otu().sniff( fname )
True
>>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.otu' )
>>> Otu().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', labels (MetadataParameter): Label Names, defaults to '[]', otulabels (MetadataParameter): OTU Names, defaults to '[]'

sniff(filename)

class galaxy.datatypes.mothur.Sabund(**kwd)

Bases: galaxy.datatypes.mothur.Otu

file_ext = 'mothur.sabund'

__init__(**kwd)

http://www.mothur.org/wiki/Sabund_file

init_meta(dataset, copy_from=None)

sniff_prefix(file_prefix)

Determines whether the file is otu (operational taxonomic unit) format label<TAB>count[<TAB>value(1..n)]

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.sabund' )
>>> Sabund().sniff( fname )
True
>>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.sabund' )
>>> Sabund().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', labels (MetadataParameter): Label Names, defaults to '[]', otulabels (MetadataParameter): OTU Names, defaults to '[]'

class galaxy.datatypes.mothur.GroupAbund(**kwd)

Bases: galaxy.datatypes.mothur.Otu

file_ext = 'mothur.shared'

__init__(**kwd)

init_meta(dataset, copy_from=None)

set_meta(dataset, overwrite=True, skip=1, **kwd)

sniff_prefix(file_prefix, vals_are_int=False)

Determines whether the file is a otu (operational taxonomic unit) Shared format label<TAB>group<TAB>count[<TAB>value(1..n)] The first line is column headings as of Mothur v 1.2

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.shared' )
>>> GroupAbund().sniff( fname )
True
>>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.shared' )
>>> GroupAbund().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', labels (MetadataParameter): Label Names, defaults to '[]', otulabels (MetadataParameter): OTU Names, defaults to '[]', groups (MetadataParameter): Group Names, defaults to '[]'

class galaxy.datatypes.mothur.SecondaryStructureMap(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.map'

__init__(**kwd)

Initialize secondary structure map datatype

sniff_prefix(file_prefix)

Determines whether the file is a secondary structure map format A single column with an integer value which indicates the row that this row maps to. Check to make sure if structMap[10] = 380 then structMap[380] = 10 and vice versa.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.map' )
>>> SecondaryStructureMap().sniff( fname )
True
>>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.map' )
>>> SecondaryStructureMap().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

sniff(filename)

class galaxy.datatypes.mothur.AlignCheck(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.align.check'

__init__(**kwd)

Initialize AlignCheck datatype

set_meta(dataset, overwrite=True, **kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.mothur.AlignReport(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template AY457915 501 82283 1525 kmer 89.07 needleman 5 501 1 499 499 2 0 0 97.6

file_ext = 'mothur.align.report'

__init__(**kwd)

Initialize AlignCheck datatype

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.mothur.DistanceMatrix(**kwd)

Bases: galaxy.datatypes.data.Text

file_ext = 'mothur.dist'

Add metadata elements

init_meta(dataset, copy_from=None)

set_meta(dataset, overwrite=True, skip=0, **kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequence_count (MetadataParameter): Number of sequences, defaults to '0'

class galaxy.datatypes.mothur.LowerTriangleDistanceMatrix(**kwd)

Bases: galaxy.datatypes.mothur.DistanceMatrix

file_ext = 'mothur.lower.dist'

__init__(**kwd)

Initialize secondary structure map datatype

init_meta(dataset, copy_from=None)

sniff_prefix(file_prefix)

Determines whether the file is a lower-triangle distance matrix (phylip) format The first line has the number of sequences in the matrix. The remaining lines have the sequence name followed by a list of distances from all preceeding sequences

5 # possibly but not always preceded by a tab :/ U68589 U68590 0.3371 U68591 0.3609 0.3782 U68592 0.4155 0.3197 0.4148 U68593 0.2872 0.1690 0.3361 0.2842

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.lower.dist' )
>>> LowerTriangleDistanceMatrix().sniff( fname )
True
>>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.lower.dist' )
>>> LowerTriangleDistanceMatrix().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequence_count (MetadataParameter): Number of sequences, defaults to '0'

sniff(filename)

class galaxy.datatypes.mothur.SquareDistanceMatrix(**kwd)

Bases: galaxy.datatypes.mothur.DistanceMatrix

file_ext = 'mothur.square.dist'

__init__(**kwd)

init_meta(dataset, copy_from=None)

sniff_prefix(file_prefix)

Determines whether the file is a square distance matrix (Column-formatted distance matrix) format The first line has the number of sequences in the matrix. The following lines have the sequence name in the first column plus a column for the distance to each sequence in the row order in which they appear in the matrix.

3 U68589 0.0000 0.3371 0.3610 U68590 0.3371 0.0000 0.3783 U68590 0.3371 0.0000 0.3783

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.square.dist' )
>>> SquareDistanceMatrix().sniff( fname )
True
>>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.square.dist' )
>>> SquareDistanceMatrix().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequence_count (MetadataParameter): Number of sequences, defaults to '0'

sniff(filename)

class galaxy.datatypes.mothur.PairwiseDistanceMatrix(**kwd)

Bases: galaxy.datatypes.mothur.DistanceMatrix, galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.pair.dist'

__init__(**kwd)

Initialize secondary structure map datatype

set_meta(dataset, overwrite=True, skip=None, **kwd)

sniff_prefix(file_prefix)

Determines whether the file is a pairwise distance matrix (Column-formatted distance matrix) format The first and second columns have the sequence names and the third column is the distance between those sequences.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.pair.dist' )
>>> PairwiseDistanceMatrix().sniff( fname )
True
>>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.pair.dist' )
>>> PairwiseDistanceMatrix().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequence_count (MetadataParameter): Number of sequences, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

sniff(filename)

class galaxy.datatypes.mothur.Names(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.names'

__init__(**kwd)

http://www.mothur.org/wiki/Name_file Name file shows the relationship between a representative sequence(col 1) and the sequences(comma-separated) it represents(col 2)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.mothur.Summary(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.summary'

__init__(**kwd)

summarizes the quality of sequences in an unaligned or aligned fasta-formatted sequence file

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.mothur.Group(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.groups'

__init__(**kwd)

http://www.mothur.org/wiki/Groups_file Group file assigns sequence (col 1) to a group (col 2)

set_meta(dataset, overwrite=True, skip=None, max_data_lines=None, **kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', groups (MetadataParameter): Group Names, defaults to '[]'

class galaxy.datatypes.mothur.AccNos(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.accnos'

__init__(**kwd)

A list of names

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.mothur.Oligos(**kwd)

Bases: galaxy.datatypes.data.Text

file_ext = 'mothur.oligos'

sniff_prefix(file_prefix)

http://www.mothur.org/wiki/Oligos_File Determines whether the file is a otu (operational taxonomic unit) format

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.oligos' )
>>> Oligos().sniff( fname )
True
>>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.oligos' )
>>> Oligos().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.mothur.Frequency(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.freq'

__init__(**kwd)

A list of names

sniff_prefix(file_prefix)

Determines whether the file is a frequency tabular format for chimera analysis #1.14.0 0 0.000 1 0.000 … 155 0.975

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.freq' )
>>> Frequency().sniff( fname )
True
>>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.freq' )
>>> Frequency().sniff( fname )
False
>>> # Expression count matrix (EdgeR wrapper)
>>> fname = get_test_fname( 'mothur_datatypetest_false_2.mothur.freq' )
>>> Frequency().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

sniff(filename)

class galaxy.datatypes.mothur.Quantile(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.quan'

__init__(**kwd)

Quantiles for chimera analysis

sniff_prefix(file_prefix)

Determines whether the file is a quantiles tabular format for chimera analysis 1 0 0 0 0 0 0 2 0.309198 0.309198 0.37161 0.37161 0.37161 0.37161 3 0.510982 0.563213 0.693529 0.858939 1.07442 1.20608 …

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.quan' )
>>> Quantile().sniff( fname )
True
>>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.quan' )
>>> Quantile().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', filtered (MetadataParameter): Quantiles calculated using a mask, defaults to 'False', masked (MetadataParameter): Quantiles calculated using a frequency filter, defaults to 'False'

sniff(filename)

class galaxy.datatypes.mothur.LaneMask(**kwd)

Bases: galaxy.datatypes.data.Text

file_ext = 'mothur.filter'

sniff_prefix(file_prefix)

Determines whether the file is a lane mask filter: 1 line consisting of zeros and ones.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.filter' )
>>> LaneMask().sniff( fname )
True
>>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.filter' )
>>> LaneMask().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.mothur.CountTable(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.count_table'

__init__(**kwd)

http://www.mothur.org/wiki/Count_File A table with first column names and following columns integer counts # Example 1: Representative_Sequence total U68630 1 U68595 1 U68600 1 # Example 2 (with group columns): Representative_Sequence total forest pasture U68630 1 1 0 U68595 1 1 0 U68600 1 1 0 U68591 1 1 0 U68647 1 0 1

set_meta(dataset, overwrite=True, skip=1, max_data_lines=None, **kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', groups (MetadataParameter): Group Names, defaults to '[]'

class galaxy.datatypes.mothur.RefTaxonomy(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.ref.taxonomy'

__init__(**kwd)

sniff_prefix(file_prefix)

Determines whether the file is a Reference Taxonomy

http://www.mothur.org/wiki/Taxonomy_outline A table with 2 or 3 columns: - SequenceName - Taxonomy (semicolon-separated taxonomy in descending order) - integer ? Example: 2-column (http://www.mothur.org/wiki/Taxonomy_outline)

X56533.1 Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Oligohymenophorea;Hymenostomatida;Tetrahymenina;Glaucomidae;Glaucoma; X97975.1 Eukaryota;Parabasalidea;Trichomonada;Trichomonadida;unclassified_Trichomonadida; AF052717.1 Eukaryota;Parabasalidea;

Example: 3-column (http://vamps.mbl.edu/resources/databases.php)

v3_AA008 Bacteria;Firmicutes;Bacilli;Lactobacillales;Streptococcaceae;Streptococcus 5 v3_AA016 Bacteria 120 v3_AA019 Archaea;Crenarchaeota;Marine_Group_I 1

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.ref.taxonomy' )
>>> RefTaxonomy().sniff( fname )
True
>>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.ref.taxonomy' )
>>> RefTaxonomy().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

sniff(filename)

class galaxy.datatypes.mothur.ConsensusTaxonomy(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.cons.taxonomy'

__init__(**kwd)

A list of names

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.mothur.TaxonomySummary(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.tax.summary'

__init__(**kwd)

A Summary of taxon classification

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.mothur.Axes(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.axes'

__init__(**kwd)

Initialize axes datatype

sniff_prefix(file_prefix)

Determines whether the file is an axes format The first line may have column headings. The following lines have the name in the first column plus float columns for each axis. ==> 98_sq_phylip_amazon.fn.unique.pca.axes <==

group axis1 axis2 forest 0.000000 0.145743 pasture 0.145743 0.000000

==> 98_sq_phylip_amazon.nmds.axes <==

axis1 axis2

U68589 0.262608 -0.077498 U68590 0.027118 0.195197 U68591 0.329854 0.014395

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'mothur_datatypetest_true.mothur.axes' )
>>> Axes().sniff( fname )
True
>>> fname = get_test_fname( 'mothur_datatypetest_false.mothur.axes' )
>>> Axes().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

sniff(filename)

class galaxy.datatypes.mothur.SffFlow(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'mothur.sff.flow'

http://www.mothur.org/wiki/Flow_file The first line is the total number of flow values - 800 for Titanium data. For GS FLX it would be 400. Following lines contain: - SequenceName - the number of useable flows as defined by 454’s software - the flow intensity for each base going in the order of TACG. Example:

800 GQY1XT001CQL4K 85 1.04 0.00 1.00 0.02 0.03 1.02 0.05 … GQY1XT001CQIRF 84 1.02 0.06 0.98 0.06 0.09 1.05 0.07 … GQY1XT001CF5YW 88 1.02 0.02 1.01 0.04 0.06 1.02 0.03 …

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', flow_values (MetadataParameter): Total number of flow values, defaults to '', flow_order (MetadataParameter): Total number of flow values, defaults to 'TACG'

set_meta(dataset, overwrite=True, skip=1, max_data_lines=None, **kwd)

make_html_table(dataset, skipchars=[])

Create HTML table, used for displaying peek

galaxy.datatypes.msa module

class galaxy.datatypes.msa.InfernalCM(**kwd)

Bases: galaxy.datatypes.data.Text

file_ext = 'cm'

set_peek(dataset, is_multi_byte=False)

sniff_prefix(file_prefix)

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'infernal_model.cm' )
>>> InfernalCM().sniff( fname )
True
>>> fname = get_test_fname( '2.txt' )
>>> InfernalCM().sniff( fname )
False

set_meta(dataset, **kwd)

Set the number of models and the version of CM file in dataset.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', number_of_models (MetadataParameter): Number of covariance models, defaults to '0', cm_version (MetadataParameter): Infernal Covariance Model version, defaults to '1/a'

sniff(filename)

class galaxy.datatypes.msa.Hmmer(**kwd)

Bases: galaxy.datatypes.data.Text

edam_data = 'data_1364'

edam_format = 'format_1370'

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

sniff_prefix(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.msa.Hmmer2(**kwd)

Bases: galaxy.datatypes.msa.Hmmer

edam_format = 'format_3328'

file_ext = 'hmm2'

sniff_prefix(file_prefix)

HMMER2 files start with HMMER2.0

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.msa.Hmmer3(**kwd)

Bases: galaxy.datatypes.msa.Hmmer

edam_format = 'format_3329'

file_ext = 'hmm3'

sniff_prefix(file_prefix)

HMMER3 files start with HMMER3/f

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.msa.HmmerPress(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class for hmmpress database files.

file_ext = 'hmmpress'

allow_datatype_change = False

composite_type = 'basic'

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text.

display_peek(dataset)

Create HTML content, used for displaying peek.

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.msa.Stockholm_1_0(**kwd)

Bases: galaxy.datatypes.data.Text

edam_data = 'data_0863'

edam_format = 'format_1961'

file_ext = 'stockholm'

set_peek(dataset, is_multi_byte=False)

sniff_prefix(file_prefix)

set_meta(dataset, **kwd)

Set the number of models in dataset.

classmethod split(input_datasets, subdir_generator_function, split_params)

Split the input files by model records.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', number_of_models (MetadataParameter): Number of multiple alignments, defaults to '0'

sniff(filename)

class galaxy.datatypes.msa.MauveXmfa(**kwd)

Bases: galaxy.datatypes.data.Text

file_ext = 'xmfa'

set_peek(dataset, is_multi_byte=False)

sniff_prefix(file_prefix)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', number_of_models (MetadataParameter): Number of alignmened sequences, defaults to '0'

set_meta(dataset, **kwd)

sniff(filename)

galaxy.datatypes.neo4j module

Neo4j Composite Dataset

class galaxy.datatypes.neo4j.Neo4j(**kwd)

Bases: galaxy.datatypes.images.Html

base class to use for neostore datatypes derived from html - composite datatype elements stored in extra files path

generate_primary_file(dataset=None)

This is called only at upload to write the html file cannot rename the datasets here - they come with the default unfortunately

get_mime()

Returns the mime type of the datatype

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

display_peek(dataset)

Create HTML content, used for displaying peek.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.neo4j.Neo4jDB(**kwd)

Bases: galaxy.datatypes.neo4j.Neo4j, galaxy.datatypes.data.Data

Class for neo4jDB database files.

file_ext = 'neostore'

composite_type = 'auto_primary_file'

allow_datatype_change = False

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.neo4j.Neo4jDBzip(**kwd)

Bases: galaxy.datatypes.neo4j.Neo4j, galaxy.datatypes.data.Data

Class for neo4jDB database files.

file_ext = 'neostore.zip'

composite_type = 'auto_primary_file'

allow_datatype_change = False

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', reference_name (MetadataParameter): Reference Name, defaults to 'neostore_file', neostore_zip (MetadataParameter): Neostore zip, defaults to 'None'

galaxy.datatypes.ngsindex module

NGS indexes

class galaxy.datatypes.ngsindex.BowtieIndex(**kwd)

Bases: galaxy.datatypes.text.Html

base class for BowtieIndex is subclassed by BowtieColorIndex and BowtieBaseIndex

composite_type = 'auto_primary_file'

allow_datatype_change = False

generate_primary_file(dataset=None)

This is called only at upload to write the html file cannot rename the datasets here - they come with the default unfortunately

regenerate_primary_file(dataset)

cannot do this until we are setting metadata

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for this index set, defaults to 'galaxy_generated_bowtie_index', sequence_space (MetadataParameter): sequence_space for this index set, defaults to 'unknown'

class galaxy.datatypes.ngsindex.BowtieColorIndex(**kwd)

Bases: galaxy.datatypes.ngsindex.BowtieIndex

Bowtie color space index

file_ext = 'bowtie_color_index'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for this index set, defaults to 'galaxy_generated_bowtie_index', sequence_space (MetadataParameter): sequence_space for this index set, defaults to 'color'

class galaxy.datatypes.ngsindex.BowtieBaseIndex(**kwd)

Bases: galaxy.datatypes.ngsindex.BowtieIndex

Bowtie base space index

file_ext = 'bowtie_base_index'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', base_name (MetadataParameter): base name for this index set, defaults to 'galaxy_generated_bowtie_index', sequence_space (MetadataParameter): sequence_space for this index set, defaults to 'base'

galaxy.datatypes.phylip module

Created on January. 05, 2018

@authors: Kenzo-Hugo Hillion and Fabien Mareuil, Institut Pasteur, Paris @contacts: kehillio@pasteur.fr and fabien.mareuil@pasteur.fr @project: galaxy @githuborganization: C3BI Phylip datatype sniffer

class galaxy.datatypes.phylip.Phylip(**kwd)

Bases: galaxy.datatypes.data.Text

Phylip format stores a multiple sequence alignment

edam_data = 'data_0863'

edam_format = 'format_1997'

file_ext = 'phylip'

Add metadata elements

set_meta(dataset, **kwd)

Set the number of sequences and the number of data lines in dataset.

set_peek(dataset, is_multi_byte=False)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequences (MetadataParameter): Number of sequences, defaults to '0'

sniff(filename)

sniff_prefix(file_prefix)

All Phylip files starts with the number of sequences so we can use this to count the following number of sequences in the first ‘stack’

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.phylip')
>>> Phylip().sniff(fname)
True

galaxy.datatypes.plant_tribes module

class galaxy.datatypes.plant_tribes.Smat(**kwd)

Bases: galaxy.datatypes.data.Text

file_ext = 'smat'

display_peek(dataset)

set_peek(dataset, is_multi_byte=False)

sniff_prefix(file_prefix)

The use of ESTScan implies the creation of scores matrices which reflect the codons preferences in the studied organisms. The ESTScan package includes scripts for generating these files. The output of these scripts consists of the matrices, one for each isochor, and which look like this:

FORMAT: hse_4is.conf CODING REGION 6 3 1 s C+G: 0 44 -1 0 2 -2 2 1 -8 0

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test_space.txt')
>>> Smat().sniff(fname)
False
>>> fname = get_test_fname('test_tab.bed')
>>> Smat().sniff(fname)
False
>>> fname = get_test_fname('1.smat')
>>> Smat().sniff(fname)
True

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.plant_tribes.PlantTribesKsComponents(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'ptkscmp'

display_peek(dataset)

set_meta(dataset, **kwd)

Set the number of significant components in the Ks distribution. The dataset will always be on the order of less than 10 lines.

set_peek(dataset, is_multi_byte=False)

sniff(filename)

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test_tab.bed')
>>> PlantTribesKsComponents().sniff(fname)
False
>>> fname = get_test_fname('1.ptkscmp')
>>> PlantTribesKsComponents().sniff(fname)
True

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', number_comp (MetadataParameter): Number of significant components in the Ks distribution, defaults to '0'

galaxy.datatypes.proteomics module

Proteomics Datatypes

class galaxy.datatypes.proteomics.Wiff(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class for wiff files.

edam_data = 'data_2536'

edam_format = 'format_3710'

file_ext = 'wiff'

allow_datatype_change = False

composite_type = 'auto_primary_file'

__init__(**kwd)

generate_primary_file(dataset=None)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.proteomics.PepXmlReport(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

pepxml converted to tabular report

edam_data = 'data_2536'

file_ext = 'pepxml.tsv'

__init__(**kwd)

display_peek(dataset)

Returns formated html of peek

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.proteomics.ProtXmlReport(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

protxml converted to tabular report

edam_data = 'data_2536'

file_ext = 'protxml.tsv'

comment_lines = 1

__init__(**kwd)

display_peek(dataset)

Returns formated html of peek

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.proteomics.ProteomicsXml(**kwd)

Bases: galaxy.datatypes.xml.GenericXml

An enhanced XML datatype used to reuse code across several proteomic/mass-spec datatypes.

edam_data = 'data_2536'

edam_format = 'format_2032'

sniff_prefix(file_prefix)

Determines whether the file is the correct XML type.

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.PepXml(**kwd)

Bases: galaxy.datatypes.proteomics.ProteomicsXml

pepXML data

edam_format = 'format_3655'

file_ext = 'pepxml'

blurb = 'pepXML data'

root = 'msms_pipeline_analysis'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.MzML(**kwd)

Bases: galaxy.datatypes.proteomics.ProteomicsXml

mzML data

edam_format = 'format_3244'

file_ext = 'mzml'

blurb = 'mzML Mass Spectrometry data'

root = '(mzML|indexedmzML)'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.ProtXML(**kwd)

Bases: galaxy.datatypes.proteomics.ProteomicsXml

protXML data

file_ext = 'protxml'

blurb = 'prot XML Search Results'

root = 'protein_summary'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.MzXML(**kwd)

Bases: galaxy.datatypes.proteomics.ProteomicsXml

mzXML data

edam_format = 'format_3654'

file_ext = 'mzxml'

blurb = 'mzXML Mass Spectrometry data'

root = 'mzXML'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.MzData(**kwd)

Bases: galaxy.datatypes.proteomics.ProteomicsXml

mzData data

edam_format = 'format_3245'

file_ext = 'mzdata'

blurb = 'mzData Mass Spectrometry data'

root = 'mzData'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.MzIdentML(**kwd)

Bases: galaxy.datatypes.proteomics.ProteomicsXml

edam_format = 'format_3247'

file_ext = 'mzid'

blurb = 'XML identified peptides and proteins.'

root = 'MzIdentML'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.TraML(**kwd)

Bases: galaxy.datatypes.proteomics.ProteomicsXml

edam_format = 'format_3246'

file_ext = 'traml'

blurb = 'TraML transition list'

root = 'TraML'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.MzQuantML(**kwd)

Bases: galaxy.datatypes.proteomics.ProteomicsXml

edam_format = 'format_3248'

file_ext = 'mzq'

blurb = 'XML quantification data'

root = 'MzQuantML'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.ConsensusXML(**kwd)

Bases: galaxy.datatypes.proteomics.ProteomicsXml

file_ext = 'consensusxml'

blurb = 'OpenMS multiple LC-MS map alignment file'

root = 'consensusXML'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.FeatureXML(**kwd)

Bases: galaxy.datatypes.proteomics.ProteomicsXml

file_ext = 'featurexml'

blurb = 'OpenMS feature file'

root = 'featureMap'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.IdXML(**kwd)

Bases: galaxy.datatypes.proteomics.ProteomicsXml

file_ext = 'idxml'

blurb = 'OpenMS identification file'

root = 'IdXML'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.TandemXML(**kwd)

Bases: galaxy.datatypes.proteomics.ProteomicsXml

edam_format = 'format_3711'

file_ext = 'tandem'

blurb = 'X!Tandem search results file'

root = 'bioml'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.UniProtXML(**kwd)

Bases: galaxy.datatypes.proteomics.ProteomicsXml

file_ext = 'uniprotxml'

blurb = 'UniProt Proteome file'

root = 'uniprot'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.Mgf(**kwd)

Bases: galaxy.datatypes.data.Text

Mascot Generic Format data

edam_data = 'data_2536'

edam_format = 'format_3651'

file_ext = 'mgf'

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.MascotDat(**kwd)

Bases: galaxy.datatypes.data.Text

Mascot search results

edam_data = 'data_2536'

edam_format = 'format_3713'

file_ext = 'mascotdat'

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.ThermoRAW(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing a Thermo Finnigan binary RAW file

edam_data = 'data_2536'

edam_format = 'format_3712'

file_ext = 'raw'

sniff(filename)

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.proteomics.Msp(**kwd)

Bases: galaxy.datatypes.data.Text

Output of NIST MS Search Program chemdata.nist.gov/mass-spc/ftp/mass-spc/PepLib.pdf

file_ext = 'msp'

static next_line_starts_with(contents, prefix)

sniff_prefix(file_prefix)

Determines whether the file is a NIST MSP output file.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.proteomics.SPLibNoIndex(**kwd)

Bases: galaxy.datatypes.data.Text

SPlib without index file

file_ext = 'splib_noindex'

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.proteomics.SPLib(**kwd)

Bases: galaxy.datatypes.proteomics.Msp

SpectraST Spectral Library. Closely related to msp format

file_ext = 'splib'

composite_type = 'auto_primary_file'

__init__(**kwd)

generate_primary_file(dataset=None)

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

sniff_prefix(file_prefix)

Determines whether the file is a SpectraST generated file.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.proteomics.Ms2(**kwd)

Bases: galaxy.datatypes.data.Text

file_ext = 'ms2'

sniff_prefix(file_prefix)

Determines whether the file is a valid ms2 file.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.proteomics.XHunterAslFormat(**kwd)

Bases: galaxy.datatypes.binary.Binary

Annotated Spectra in the HLF format http://www.thegpm.org/HUNTER/format_2006_09_15.html

file_ext = 'hlf'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.proteomics.Sf3(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class describing a Scaffold SF3 files

file_ext = 'sf3'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.proteomics.ImzML(**kwd)

Bases: galaxy.datatypes.binary.Binary

Class for imzML files. http://www.imzml.org

edam_format = 'format_3682'

file_ext = 'imzml'

allow_datatype_change = False

composite_type = 'auto_primary_file'

__init__(**kwd)

generate_primary_file(dataset=None)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.proteomics.Analyze75(**kwd)

Bases: galaxy.datatypes.binary.Binary

Mayo Analyze 7.5 files http://www.imzml.org

file_ext = 'analyze75'

allow_datatype_change = False

composite_type = 'auto_primary_file'

__init__(**kwd)

generate_primary_file(dataset=None)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

galaxy.datatypes.qualityscore module

Qualityscore class

class galaxy.datatypes.qualityscore.QualityScore(**kwd)

Bases: galaxy.datatypes.data.Text

until we know more about quality score formats

edam_data = 'data_2048'

edam_format = 'format_3606'

file_ext = 'qual'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.qualityscore.QualityScoreSOLiD(**kwd)

Bases: galaxy.datatypes.qualityscore.QualityScore

until we know more about quality score formats

edam_format = 'format_3610'

file_ext = 'qualsolid'

sniff_prefix(file_prefix)

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'sequence.fasta' )
>>> QualityScoreSOLiD().sniff( fname )
False
>>> fname = get_test_fname( 'sequence.qualsolid' )
>>> QualityScoreSOLiD().sniff( fname )
True

set_meta(dataset, **kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.qualityscore.QualityScore454(**kwd)

Bases: galaxy.datatypes.qualityscore.QualityScore

until we know more about quality score formats

edam_format = 'format_3611'

file_ext = 'qual454'

sniff_prefix(file_prefix)

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'sequence.fasta' )
>>> QualityScore454().sniff( fname )
False
>>> fname = get_test_fname( 'sequence.qual454' )
>>> QualityScore454().sniff( fname )
True

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.qualityscore.QualityScoreSolexa(**kwd)

Bases: galaxy.datatypes.qualityscore.QualityScore

until we know more about quality score formats

edam_format = 'format_3608'

file_ext = 'qualsolexa'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.qualityscore.QualityScoreIllumina(**kwd)

Bases: galaxy.datatypes.qualityscore.QualityScore

until we know more about quality score formats

edam_format = 'format_3609'

file_ext = 'qualillumina'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

galaxy.datatypes.registry module

Provides mapping between extensions and datatypes, mime-types, etc.

exception galaxy.datatypes.registry.ConfigurationError

Bases: exceptions.Exception

class galaxy.datatypes.registry.Registry(config=None)

Bases: object

__init__(config=None)

load_datatypes(root_dir=None, config=None, deactivate=False, override=True)

Parse a datatypes XML file located at root_dir/config (if processing the Galaxy distributed config) or contained within an installed Tool Shed repository. If deactivate is True, an installed Tool Shed repository that includes custom datatypes is being deactivated or uninstalled, so appropriate loaded datatypes will be removed from the registry. The value of override will be False when a Tool Shed repository is being installed. Since installation is occurring after the datatypes registry has been initialized at server startup, its contents cannot be overridden by newly introduced conflicting data types.

get_legacy_sites_by_build(site_type, build)

get_display_sites(site_type)

load_datatype_sniffers(root, deactivate=False, handling_proprietary_datatypes=False, override=False, compressed_sniffers=None)

Process the sniffers element from a parsed a datatypes XML file located at root_dir/config (if processing the Galaxy distributed config) or contained within an installed Tool Shed repository. If deactivate is True, an installed Tool Shed repository that includes custom sniffers is being deactivated or uninstalled, so appropriate loaded sniffers will be removed from the registry. The value of override will be False when a Tool Shed repository is being installed. Since installation is occurring after the datatypes registry has been initialized at server startup, its contents cannot be overridden by newly introduced conflicting sniffers.

is_extension_unsniffable_binary(ext)

get_datatype_class_by_name(name)

Return the datatype class where the datatype’s type attribute (as defined in the datatype_conf.xml file) contains name.

get_available_tracks()

get_mimetype_by_extension(ext, default='application/octet-stream')

Returns a mimetype based on an extension

get_datatype_by_extension(ext)

Returns a datatype object based on an extension

change_datatype(data, ext)

load_datatype_converters(toolbox, installed_repository_dict=None, deactivate=False, use_cached=False)

If deactivate is False, add datatype converters from self.converters or self.proprietary_converters to the calling app’s toolbox. If deactivate is True, eliminates relevant converters from the calling app’s toolbox.

load_display_applications(app, installed_repository_dict=None, deactivate=False)

If deactivate is False, add display applications from self.display_app_containers or self.proprietary_display_app_containers to appropriate datatypes. If deactivate is True, eliminates relevant display applications from appropriate datatypes.

reload_display_applications(display_application_ids=None)

Reloads display applications: by id, or all if no ids provided Returns tuple( [reloaded_ids], [failed_ids] )

load_external_metadata_tool(toolbox)

Adds a tool which is used to set external metadata

set_default_values()

get_converters_by_datatype(ext)

Returns available converters by source type

get_converter_by_target_type(source_ext, target_ext)

Returns a converter based on source and target datatypes

find_conversion_destination_for_dataset_by_extensions(dataset_or_ext, accepted_formats, converter_safe=True)

Returns ( target_ext, existing converted dataset )

get_composite_extensions()

get_upload_metadata_params(context, group, tool)

Returns dict of case value:inputs for metadata conditional for upload tool

edam_formats

edam_data

to_xml_file(path)

get_extension(elem)

Function which returns the extension lowercased :param elem: :return extension:

galaxy.datatypes.registry.example_datatype_registry_for_sample(sniff_compressed_dynamic_datatypes_default=True)

galaxy.datatypes.sequence module

Sequence classes

class galaxy.datatypes.sequence.SequenceSplitLocations(**kwd)

Bases: galaxy.datatypes.data.Text

Class storing information about a sequence file composed of multiple gzip files concatenated as one OR an uncompressed file. In the GZIP case, each sub-file’s location is stored in start and end.

The format of the file is JSON:

{ "sections" : [
        { "start" : "x", "end" : "y", "sequences" : "z" },
        ...
]}

file_ext = 'fqtoc'

set_peek(dataset, is_multi_byte=False)

sniff_prefix(file_prefix)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.sequence.Sequence(**kwd)

Bases: galaxy.datatypes.data.Text

Class describing a sequence

edam_data = 'data_2044'

Add metadata elements

set_meta(dataset, **kwd)

Set the number of sequences and the number of data lines in dataset.

set_peek(dataset, is_multi_byte=False)

static get_sequences_per_file(total_sequences, split_params)

classmethod do_slow_split(input_datasets, subdir_generator_function, split_params)

classmethod do_fast_split(input_datasets, toc_file_datasets, subdir_generator_function, split_params)

classmethod write_split_files(input_datasets, toc_file_datasets, subdir_generator_function, sequences_per_file)

split(input_datasets, subdir_generator_function, split_params)

Split a generic sequence file (not sensible or possible, see subclasses).

static get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count)

Uses a Table of Contents dict, parsed from an FQTOC file, to come up with a set of shell commands that will extract the parts necessary >>> three_sections=[dict(start=0, end=74, sequences=10), dict(start=74, end=148, sequences=10), dict(start=148, end=148+76, sequences=10)] >>> Sequence.get_split_commands_with_toc(‘./input.gz’, ‘./output.gz’, dict(sections=three_sections), start_sequence=0, sequence_count=10) [‘dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null >> ./output.gz’] >>> Sequence.get_split_commands_with_toc(‘./input.gz’, ‘./output.gz’, dict(sections=three_sections), start_sequence=1, sequence_count=5) [‘(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +5 2> /dev/null) | head -20 | gzip -c >> ./output.gz’] >>> Sequence.get_split_commands_with_toc(‘./input.gz’, ‘./output.gz’, dict(sections=three_sections), start_sequence=0, sequence_count=20) [‘dd bs=1 skip=0 count=148 if=./input.gz 2> /dev/null >> ./output.gz’] >>> Sequence.get_split_commands_with_toc(‘./input.gz’, ‘./output.gz’, dict(sections=three_sections), start_sequence=5, sequence_count=10) [‘(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +21 2> /dev/null) | head -20 | gzip -c >> ./output.gz’, ‘(dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +1 2> /dev/null) | head -20 | gzip -c >> ./output.gz’] >>> Sequence.get_split_commands_with_toc(‘./input.gz’, ‘./output.gz’, dict(sections=three_sections), start_sequence=10, sequence_count=10) [‘dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null >> ./output.gz’] >>> Sequence.get_split_commands_with_toc(‘./input.gz’, ‘./output.gz’, dict(sections=three_sections), start_sequence=5, sequence_count=20) [‘(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +21 2> /dev/null) | head -20 | gzip -c >> ./output.gz’, ‘dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null >> ./output.gz’, ‘(dd bs=1 skip=148 count=76 if=./input.gz 2> /dev/null )| zcat | ( tail -n +1 2> /dev/null) | head -20 | gzip -c >> ./output.gz’]

static get_split_commands_sequential(is_compressed, input_name, output_name, start_sequence, sequence_count)

Does a brain-dead sequential scan & extract of certain sequences >>> Sequence.get_split_commands_sequential(True, ‘./input.gz’, ‘./output.gz’, start_sequence=0, sequence_count=10) [‘zcat “./input.gz” | ( tail -n +1 2> /dev/null) | head -40 | gzip -c > “./output.gz”’] >>> Sequence.get_split_commands_sequential(False, ‘./input.fastq’, ‘./output.fastq’, start_sequence=10, sequence_count=10) [‘tail -n +41 “./input.fastq” 2> /dev/null | head -40 > “./output.fastq”’]

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequences (MetadataParameter): Number of sequences, defaults to '0'

class galaxy.datatypes.sequence.Alignment(**kwd)

Bases: galaxy.datatypes.data.Text

Class describing an alignment

edam_data = 'data_0863'

Add metadata elements

split(input_datasets, subdir_generator_function, split_params)

Split a generic alignment file (not sensible or possible, see subclasses).

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', species (SelectParameter): Species, defaults to '[]'

class galaxy.datatypes.sequence.Fasta(**kwd)

Bases: galaxy.datatypes.sequence.Sequence

Class representing a FASTA sequence

edam_format = 'format_1929'

file_ext = 'fasta'

sniff_prefix(file_prefix)

Determines whether the file is in fasta format

A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (“>”) symbol in the first column. All lines should be shorter than 80 characters

For complete details see http://www.ncbi.nlm.nih.gov/blast/fasta.shtml

Rules for sniffing as True:

We don’t care about line length (other than empty lines).

The first non-empty line must start with ‘>’ and the Very Next line.strip() must have sequence data and not be a header.

‘sequence data’ here is loosely defined as non-empty lines which do not start with ‘>’

This will cause Color Space FASTA (csfasta) to be detected as True (they are, after all, still FASTA files - they have a header line followed by sequence data)

Previously this method did some checking to determine if the sequence data had integers (presumably to differentiate between fasta and csfasta)

This should be done through sniff order, where csfasta (currently has a null sniff function) is detected for first (stricter definition) followed sometime after by fasta

We will only check that the first purported sequence is correctly formatted.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'sequence.maf' )
>>> Fasta().sniff( fname )
False
>>> fname = get_test_fname( 'sequence.fasta' )
>>> Fasta().sniff( fname )
True

classmethod split(input_datasets, subdir_generator_function, split_params)

Split a FASTA file sequence by sequence.

Note that even if split_mode=”number_of_parts”, the actual number of sub-files produced may not match that requested by split_size.

If split_mode=”to_size” then split_size is treated as the number of FASTA records to put in each sub-file (not size in bytes).

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequences (MetadataParameter): Number of sequences, defaults to '0'

sniff(filename)

class galaxy.datatypes.sequence.csFasta(**kwd)

Bases: galaxy.datatypes.sequence.Sequence

Class representing the SOLID Color-Space sequence ( csfasta )

edam_format = 'format_3589'

file_ext = 'csfasta'

sniff_prefix(file_prefix)

Color-space sequence:

>2_15_85_F3 T213021013012303002332212012112221222112212222

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'sequence.fasta' )
>>> csFasta().sniff( fname )
False
>>> fname = get_test_fname( 'sequence.csfasta' )
>>> csFasta().sniff( fname )
True

set_meta(dataset, **kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequences (MetadataParameter): Number of sequences, defaults to '0'

sniff(filename)

class galaxy.datatypes.sequence.BaseFastq(**kwd)

Bases: galaxy.datatypes.sequence.Sequence

Base class for FastQ sequences

edam_format = 'format_1930'

file_ext = 'fastq'

set_meta(dataset, **kwd)

Set the number of sequences and the number of data lines in dataset. FIXME: This does not properly handle line wrapping

sniff_prefix(file_prefix)

Determines whether the file is in generic fastq format For details, see http://maq.sourceforge.net/fastq.shtml

Note: There are three kinds of FASTQ files, known as “Sanger” (sometimes called “Standard”), Solexa, and Illumina

These differ in the representation of the quality scores

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( '1.fastqsanger' )
>>> FastqSanger().sniff( fname )
True
>>> fname = get_test_fname( '2.fastqsanger' )
>>> FastqSanger().sniff( fname )
True
>>> fname = get_test_fname( '2.fastq' )
>>> Fastq().sniff( fname )
True
>>> FastqSanger().sniff( fname )
False

display_data(trans, dataset, preview=False, filename=None, to_ext=None, **kwd)

classmethod split(input_datasets, subdir_generator_function, split_params)

FASTQ files are split on cluster boundaries, in increments of 4 lines

static process_split_file(data)

This is called in the context of an external process launched by a Task (possibly not on the Galaxy machine) to create the input files for the Task. The parameters: data - a dict containing the contents of the split file

static sangerQualities(lines)

Presuming lines are lines from a fastq file, return True if the qualities are compatible with sanger encoding

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequences (MetadataParameter): Number of sequences, defaults to '0'

sniff(filename)

class galaxy.datatypes.sequence.Fastq(**kwd)

Bases: galaxy.datatypes.sequence.BaseFastq

Class representing a generic FASTQ sequence

edam_format = 'format_1930'

file_ext = 'fastq'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequences (MetadataParameter): Number of sequences, defaults to '0'

class galaxy.datatypes.sequence.FastqSanger(**kwd)

Bases: galaxy.datatypes.sequence.Fastq

Class representing a FASTQ sequence ( the Sanger variant )

edam_format = 'format_1932'

file_ext = 'fastqsanger'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequences (MetadataParameter): Number of sequences, defaults to '0'

class galaxy.datatypes.sequence.FastqSolexa(**kwd)

Bases: galaxy.datatypes.sequence.Fastq

Class representing a FASTQ sequence ( the Solexa variant )

edam_format = 'format_1933'

file_ext = 'fastqsolexa'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequences (MetadataParameter): Number of sequences, defaults to '0'

class galaxy.datatypes.sequence.FastqIllumina(**kwd)

Bases: galaxy.datatypes.sequence.Fastq

Class representing a FASTQ sequence ( the Illumina 1.3+ variant )

edam_format = 'format_1931'

file_ext = 'fastqillumina'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequences (MetadataParameter): Number of sequences, defaults to '0'

class galaxy.datatypes.sequence.FastqCSSanger(**kwd)

Bases: galaxy.datatypes.sequence.Fastq

Class representing a Color Space FASTQ sequence ( e.g a SOLiD variant )

file_ext = 'fastqcssanger'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequences (MetadataParameter): Number of sequences, defaults to '0'

class galaxy.datatypes.sequence.Maf(**kwd)

Bases: galaxy.datatypes.sequence.Alignment

Class describing a Maf alignment

edam_format = 'format_3008'

file_ext = 'maf'

init_meta(dataset, copy_from=None)

set_meta(dataset, overwrite=True, **kwd)

Parses and sets species, chromosomes, index from MAF file.

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

Returns formated html of peek

make_html_table(dataset, skipchars=[])

Create HTML table, used for displaying peek

sniff_prefix(file_prefix)

Determines wether the file is in maf format

The .maf format is line-oriented. Each multiple alignment ends with a blank line. Each sequence in an alignment is on a single line, which can get quite long, but there is no length limit. Words in a line are delimited by any white space. Lines starting with # are considered to be comments. Lines starting with ## can be ignored by most programs, but contain meta-data of one form or another.

The first line of a .maf file begins with ##maf. This word is followed by white-space-separated variable=value pairs. There should be no white space surrounding the “=”.

For complete details see http://genome.ucsc.edu/FAQ/FAQformat#format5

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'sequence.maf' )
>>> Maf().sniff( fname )
True
>>> fname = get_test_fname( 'sequence.fasta' )
>>> Maf().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', species (SelectParameter): Species, defaults to '[]', blocks (MetadataParameter): Number of blocks, defaults to '0', species_chromosomes (FileParameter): Species Chromosomes, defaults to 'None', maf_index (FileParameter): MAF Index File, defaults to 'None'

sniff(filename)

class galaxy.datatypes.sequence.MafCustomTrack(**kwd)

Bases: galaxy.datatypes.data.Text

file_ext = 'mafcustomtrack'

set_meta(dataset, overwrite=True, **kwd)

Parses and sets viewport metadata from MAF file.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', vp_chromosome (MetadataParameter): Viewport Chromosome, defaults to 'chr1', vp_start (MetadataParameter): Viewport Start, defaults to '1', vp_end (MetadataParameter): Viewport End, defaults to '100'

class galaxy.datatypes.sequence.Axt(**kwd)

Bases: galaxy.datatypes.data.Text

Class describing an axt alignment

edam_data = 'data_0863'

edam_format = 'format_3013'

file_ext = 'axt'

sniff_prefix(file_prefix)

Determines whether the file is in axt format

axt alignment files are produced from Blastz, an alignment tool available from Webb Miller’s lab at Penn State University.

Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines.

The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields.

The sequence lines contain the sequence of the primary assembly (line 2) and aligning assembly (line 3) with inserts. Repeats are indicated by lower-case letters.

For complete details see http://genome.ucsc.edu/goldenPath/help/axt.html

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'alignment.axt' )
>>> Axt().sniff( fname )
True
>>> fname = get_test_fname( 'alignment.lav' )
>>> Axt().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.sequence.Lav(**kwd)

Bases: galaxy.datatypes.data.Text

Class describing a LAV alignment

edam_data = 'data_0863'

edam_format = 'format_3014'

file_ext = 'lav'

sniff_prefix(file_prefix)

Determines whether the file is in lav format

LAV is an alignment format developed by Webb Miller’s group. It is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav.

For complete details see http://www.bioperl.org/wiki/LAV_alignment_format

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'alignment.lav' )
>>> Lav().sniff( fname )
True
>>> fname = get_test_fname( 'alignment.axt' )
>>> Lav().sniff( fname )
False

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.sequence.RNADotPlotMatrix(**kwd)

Bases: galaxy.datatypes.data.Data

edam_format = 'format_3466'

file_ext = 'rna_eps'

set_peek(dataset, is_multi_byte=False)

sniff(filename)

Determine if the file is in RNA dot plot format.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.sequence.DotBracket(**kwd)

Bases: galaxy.datatypes.sequence.Sequence

edam_data = 'data_0880'

edam_format = 'format_1457'

file_ext = 'dbn'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequences (MetadataParameter): Number of sequences, defaults to '0'

sniff(filename)

sequence_regexp = <_sre.SRE_Pattern object>

structure_regexp = <_sre.SRE_Pattern object>

set_meta(dataset, **kwd)

Set the number of sequences and the number of data lines in dataset.

sniff_prefix(file_prefix)

Galaxy Dbn (Dot-Bracket notation) rules:

• The first non-empty line is a header line: no comment lines are allowed.

  • A header line starts with a ‘>’ symbol and continues with 0 or multiple symbols until the line ends.

• The second non-empty line is a sequence line.

  • A sequence line may only include chars that match the FASTA format (https://en.wikipedia.org/wiki/FASTA_format#Sequence_representation) symbols for nucleotides: ACGTURYKMSWBDHVN, and may thus not include whitespaces.
  • A sequence line has no prefix and no suffix.
  • A sequence line is case insensitive.

• The third non-empty line is a structure (Dot-Bracket) line and only describes the 2D structure of the sequence above it.

  • A structure line must consist of the following chars: ‘.{}[]()’.
  • A structure line must be of the same length as the sequence line, and each char represents the structure of the nucleotide above it.
  • A structure line has no prefix and no suffix.
  • A nucleotide pairs with only 1 or 0 other nucleotides.
    • In a structure line, the number of ‘(‘ symbols equals the number of ‘)’ symbols, the number of ‘[‘ symbols equals the number of ‘]’ symbols and the number of ‘{‘ symbols equals the number of ‘}’ symbols.

• The format accepts multiple entries per file, given that each entry is provided as three lines: the header, sequence and structure line.

  • Sniffing is only applied on the first entry.

• Empty lines are allowed.

class galaxy.datatypes.sequence.Genbank(**kwd)

Bases: galaxy.datatypes.data.Text

Class representing a Genbank sequence

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

edam_format = 'format_1936'

edam_data = 'data_0849'

file_ext = 'genbank'

sniff_prefix(file_prefix)

Determine whether the file is in genbank format. Works for compressed files.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( '1.genbank' )
>>> Genbank().sniff( fname )
True

class galaxy.datatypes.sequence.MemePsp(**kwd)

Bases: galaxy.datatypes.sequence.Sequence

Class representing MEME Position Specific Priors

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', sequences (MetadataParameter): Number of sequences, defaults to '0'

sniff(filename)

file_ext = 'memepsp'

sniff_prefix(file_prefix)

The format of an entry in a PSP file is:

>ID WIDTH PRIORS

For complete details see http://meme-suite.org/doc/psp-format.html

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('1.memepsp')
>>> MemePsp().sniff(fname)
True
>>> fname = get_test_fname('sequence.fasta')
>>> MemePsp().sniff(fname)
False

galaxy.datatypes.sniff module

File format detector

galaxy.datatypes.sniff.get_test_fname(fname)

Returns test data filename

galaxy.datatypes.sniff.stream_url_to_file(path)

galaxy.datatypes.sniff.stream_to_open_named_file(stream, fd, filename, source_encoding=None, source_error='strict', target_encoding=None, target_error='strict')

Writes a stream to the provided file descriptor, returns the file name. Closes file descriptor

galaxy.datatypes.sniff.stream_to_file(stream, suffix='', prefix='', dir=None, text=False, **kwd)

Writes a stream to a temporary file, returns the temporary file’s name

galaxy.datatypes.sniff.convert_newlines(fname, in_place=True, tmp_dir=None, tmp_prefix='gxupload')

Converts in place a file from universal line endings to Posix line endings.

>>> fname = get_test_fname('temp.txt')
>>> with open(fname, 'wt') as fh:
...     _ = fh.write("1 2\r3 4")
>>> convert_newlines(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir())
(2, None)
>>> open(fname).read()
'1 2\n3 4\n'

galaxy.datatypes.sniff.sep2tabs(fname, in_place=True, patt='\\s+', tmp_dir=None, tmp_prefix='gxupload')

Transforms in place a ‘sep’ separated file to a tab separated one

>>> fname = get_test_fname('temp.txt')
>>> with open(fname, 'wt') as fh:
...     _ = fh.write("1 2\n3 4\n")
>>> sep2tabs(fname)
(2, None)
>>> open(fname).read()
'1\t2\n3\t4\n'

galaxy.datatypes.sniff.convert_newlines_sep2tabs(fname, in_place=True, patt='\\s+', tmp_dir=None, tmp_prefix='gxupload')

Combines above methods: convert_newlines() and sep2tabs() so that files do not need to be read twice

>>> fname = get_test_fname('temp.txt')
>>> with open(fname, 'wt') as fh:
...     _ = fh.write("1 2\r3 4")
>>> convert_newlines_sep2tabs(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir())
(2, None)
>>> open(fname).read()
'1\t2\n3\t4\n'

galaxy.datatypes.sniff.iter_headers(fname_or_file_prefix, sep, count=60, comment_designator=None)

galaxy.datatypes.sniff.get_headers(fname_or_file_prefix, sep, count=60, comment_designator=None)

Returns a list with the first ‘count’ lines split by ‘sep’, ignoring lines starting with ‘comment_designator’

>>> fname = get_test_fname('complete.bed')
>>> get_headers(fname,'\t') == [['chr7', '127475281', '127491632', 'NM_000230', '0', '+', '127486022', '127488767', '0', '3', '29,172,3225,', '0,10713,13126,'], ['chr7', '127486011', '127488900', 'D49487', '0', '+', '127486022', '127488767', '0', '2', '155,490,', '0,2399']]
True
>>> fname = get_test_fname('test.gff')
>>> get_headers(fname, '\t', count=5, comment_designator='#') == [[''], ['chr7', 'bed2gff', 'AR', '26731313', '26731437', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731491', '26731536', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731541', '26731649', '.', '+', '.', 'score'], ['chr7', 'bed2gff', 'AR', '26731659', '26731841', '.', '+', '.', 'score']]
True

galaxy.datatypes.sniff.is_column_based(fname_or_file_prefix, sep='\t', skip=0)

Checks whether the file is column based with respect to a separator (defaults to tab separator).

>>> fname = get_test_fname('test.gff')
>>> is_column_based(fname)
True
>>> fname = get_test_fname('test_tab.bed')
>>> is_column_based(fname)
True
>>> is_column_based(fname, sep=' ')
False
>>> fname = get_test_fname('test_space.txt')
>>> is_column_based(fname)
False
>>> is_column_based(fname, sep=' ')
True
>>> fname = get_test_fname('test_ensembl.tab')
>>> is_column_based(fname)
True
>>> fname = get_test_fname('test_tab1.tabular')
>>> is_column_based(fname, sep=' ', skip=0)
False
>>> fname = get_test_fname('test_tab1.tabular')
>>> is_column_based(fname)
True

galaxy.datatypes.sniff.guess_ext(fname, sniff_order, is_binary=False)

Returns an extension that can be used in the datatype factory to generate a data for the ‘fname’ file

>>> from galaxy.datatypes.registry import example_datatype_registry_for_sample
>>> datatypes_registry = example_datatype_registry_for_sample()
>>> sniff_order = datatypes_registry.sniff_order
>>> fname = get_test_fname('empty.txt')
>>> guess_ext(fname, sniff_order)
'txt'
>>> fname = get_test_fname('megablast_xml_parser_test1.blastxml')
>>> guess_ext(fname, sniff_order)
'blastxml'
>>> fname = get_test_fname('interval.interval')
>>> guess_ext(fname, sniff_order)
'interval'
>>> fname = get_test_fname('interval1.bed')
>>> guess_ext(fname, sniff_order)
'bed'
>>> fname = get_test_fname('test_tab.bed')
>>> guess_ext(fname, sniff_order)
'bed'
>>> fname = get_test_fname('sequence.maf')
>>> guess_ext(fname, sniff_order)
'maf'
>>> fname = get_test_fname('sequence.fasta')
>>> guess_ext(fname, sniff_order)
'fasta'
>>> fname = get_test_fname('1.genbank')
>>> guess_ext(fname, sniff_order)
'genbank'
>>> fname = get_test_fname('1.genbank.gz')
>>> guess_ext(fname, sniff_order)
'genbank.gz'
>>> fname = get_test_fname('file.html')
>>> guess_ext(fname, sniff_order)
'html'
>>> fname = get_test_fname('test.gtf')
>>> guess_ext(fname, sniff_order)
'gtf'
>>> fname = get_test_fname('test.gff')
>>> guess_ext(fname, sniff_order)
'gff'
>>> fname = get_test_fname('gff_version_3.gff')
>>> guess_ext(fname, sniff_order)
'gff3'
>>> fname = get_test_fname('2.txt')
>>> guess_ext(fname, sniff_order)  # 2.txt
'txt'
>>> fname = get_test_fname('2.tabular')
>>> guess_ext(fname, sniff_order)
'tabular'
>>> fname = get_test_fname('3.txt')
>>> guess_ext(fname, sniff_order)  # 3.txt
'txt'
>>> fname = get_test_fname('test_tab1.tabular')
>>> guess_ext(fname, sniff_order)
'tabular'
>>> fname = get_test_fname('alignment.lav')
>>> guess_ext(fname, sniff_order)
'lav'
>>> fname = get_test_fname('1.sff')
>>> guess_ext(fname, sniff_order)
'sff'
>>> fname = get_test_fname('1.bam')
>>> guess_ext(fname, sniff_order)
'bam'
>>> fname = get_test_fname('3unsorted.bam')
>>> guess_ext(fname, sniff_order)
'unsorted.bam'
>>> fname = get_test_fname('test.idpDB')
>>> guess_ext(fname, sniff_order)
'idpdb'
>>> fname = get_test_fname('test.mz5')
>>> guess_ext(fname, sniff_order)
'h5'
>>> fname = get_test_fname('issue1818.tabular')
>>> guess_ext(fname, sniff_order)
'tabular'
>>> fname = get_test_fname('drugbank_drugs.cml')
>>> guess_ext(fname, sniff_order)
'cml'
>>> fname = get_test_fname('q.fps')
>>> guess_ext(fname, sniff_order)
'fps'
>>> fname = get_test_fname('drugbank_drugs.inchi')
>>> guess_ext(fname, sniff_order)
'inchi'
>>> fname = get_test_fname('drugbank_drugs.mol2')
>>> guess_ext(fname, sniff_order)
'mol2'
>>> fname = get_test_fname('drugbank_drugs.sdf')
>>> guess_ext(fname, sniff_order)
'sdf'
>>> fname = get_test_fname('5e5z.pdb')
>>> guess_ext(fname, sniff_order)
'pdb'
>>> fname = get_test_fname('mothur_datatypetest_true.mothur.otu')
>>> guess_ext(fname, sniff_order)
'mothur.otu'
>>> fname = get_test_fname('mothur_datatypetest_true.mothur.lower.dist')
>>> guess_ext(fname, sniff_order)
'mothur.lower.dist'
>>> fname = get_test_fname('mothur_datatypetest_true.mothur.square.dist')
>>> guess_ext(fname, sniff_order)
'mothur.square.dist'
>>> fname = get_test_fname('mothur_datatypetest_true.mothur.pair.dist')
>>> guess_ext(fname, sniff_order)
'mothur.pair.dist'
>>> fname = get_test_fname('mothur_datatypetest_true.mothur.freq')
>>> guess_ext(fname, sniff_order)
'mothur.freq'
>>> fname = get_test_fname('mothur_datatypetest_true.mothur.quan')
>>> guess_ext(fname, sniff_order)
'mothur.quan'
>>> fname = get_test_fname('mothur_datatypetest_true.mothur.ref.taxonomy')
>>> guess_ext(fname, sniff_order)
'mothur.ref.taxonomy'
>>> fname = get_test_fname('mothur_datatypetest_true.mothur.axes')
>>> guess_ext(fname, sniff_order)
'mothur.axes'
>>> guess_ext(get_test_fname('infernal_model.cm'), sniff_order)
'cm'
>>> fname = get_test_fname('1.gg')
>>> guess_ext(fname, sniff_order)
'gg'
>>> fname = get_test_fname('diamond_db.dmnd')
>>> guess_ext(fname, sniff_order)
'dmnd'
>>> fname = get_test_fname('1.xls')
>>> guess_ext(fname, sniff_order, is_binary=True)
'excel.xls'
>>> fname = get_test_fname('biom2_sparse_otu_table_hdf5.biom')
>>> guess_ext(fname, sniff_order)
'biom2'
>>> fname = get_test_fname('454Score.pdf')
>>> guess_ext(fname, sniff_order)
'pdf'
>>> fname = get_test_fname('1.obo')
>>> guess_ext(fname, sniff_order)
'obo'
>>> fname = get_test_fname('1.arff')
>>> guess_ext(fname, sniff_order)
'arff'
>>> fname = get_test_fname('1.afg')
>>> guess_ext(fname, sniff_order)
'afg'
>>> fname = get_test_fname('1.owl')
>>> guess_ext(fname, sniff_order)
'owl'
>>> fname = get_test_fname('Acanium.hmm')
>>> guess_ext(fname, sniff_order)
'snaphmm'
>>> fname = get_test_fname('wiggle.wig')
>>> guess_ext(fname, sniff_order)
'wig'
>>> fname = get_test_fname('example.iqtree')
>>> guess_ext(fname, sniff_order)
'iqtree'
>>> fname = get_test_fname('1.stockholm')
>>> guess_ext(fname, sniff_order)
'stockholm'
>>> fname = get_test_fname('1.xmfa')
>>> guess_ext(fname, sniff_order)
'xmfa'
>>> fname = get_test_fname('test.blib')
>>> guess_ext(fname, sniff_order)
'blib'
>>> fname = get_test_fname('test.phylip')
>>> guess_ext(fname, sniff_order)
'phylip'
>>> fname = get_test_fname('1.smat')
>>> guess_ext(fname, sniff_order)
'smat'
>>> fname = get_test_fname('1.ttl')
>>> guess_ext(fname, sniff_order)
'ttl'
>>> fname = get_test_fname('1.hdt')
>>> guess_ext(fname, sniff_order, is_binary=True)
'hdt'
>>> fname = get_test_fname('1.phyloxml')
>>> guess_ext(fname, sniff_order)
'phyloxml'
>>> fname = get_test_fname('1.tiff')
>>> guess_ext(fname, sniff_order)
'tiff'
>>> fname = get_test_fname('1.fastqsanger.gz')
>>> guess_ext(fname, sniff_order)  # See test_datatype_registry for more compressed type tests.
'fastqsanger.gz'

galaxy.datatypes.sniff.run_sniffers_raw(filename_or_file_prefix, sniff_order, is_binary=False)

Run through sniffers specified by sniff_order, return None of None match.

galaxy.datatypes.sniff.zip_single_fileobj(path)

class galaxy.datatypes.sniff.FilePrefix(filename)

Bases: object

__init__(filename)

file_size

string_io()

startswith(prefix)

line_iterator()

search(pattern)

search_str(query_str)

galaxy.datatypes.sniff.build_sniff_from_prefix(klass)

galaxy.datatypes.sniff.disable_parent_class_sniffing(klass)

galaxy.datatypes.sniff.handle_compressed_file(filename, datatypes_registry, ext='auto', tmp_prefix='sniff_uncompress_', tmp_dir=None, in_place=False, check_content=True, auto_decompress=True)

Check uploaded files for compression, check compressed file contents, and uncompress if necessary.

Supports GZip, BZip2, and the first file in a Zip file.

For performance reasons, the temporary file used for uncompression is located in the same directory as the input/output file. This behavior can be changed with the tmp_dir param.

ext as returned will only be changed from the ext input param if the param was an autodetect type (auto) and the file was sniffed as a keep-compressed datatype.

is_valid as returned will only be set if the file is compressed and contains invalid contents (or the first file in the case of a zip file), this is so lengthy decompression can be bypassed if there is invalid content in the first 32KB. Otherwise the caller should be checking content.

galaxy.datatypes.sniff.handle_uploaded_dataset_file(*args, **kwds)

Legacy wrapper about handle_uploaded_dataset_file_internal for tools using it.

galaxy.datatypes.sniff.handle_uploaded_dataset_file_internal(filename, datatypes_registry, ext='auto', tmp_prefix='sniff_upload_', tmp_dir=None, in_place=False, check_content=True, is_binary=None, auto_decompress=True, uploaded_file_ext=None, convert_to_posix_lines=None, convert_spaces_to_tabs=None)

exception galaxy.datatypes.sniff.InappropriateDatasetContentError

Bases: exceptions.Exception

galaxy.datatypes.tabular module

Tabular datatype

class galaxy.datatypes.tabular.TabularData(**kwd)

Bases: galaxy.datatypes.data.Text

Generic tabular data

edam_format = 'format_3475'

CHUNKABLE = True

Add metadata elements

set_meta(dataset, **kwd)

set_peek(dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=None)

displayable(dataset)

get_chunk(trans, dataset, offset=0, ck_size=None)

display_data(trans, dataset, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd)

make_html_table(dataset, **kwargs)

Create HTML table, used for displaying peek

make_html_peek_header(dataset, skipchars=None, column_names=None, column_number_format='%s', column_parameter_alias=None, **kwargs)

make_html_peek_rows(dataset, skipchars=None, **kwargs)

display_peek(dataset)

Returns formatted html of peek

column_dataprovider(*args, **kwargs)

Uses column settings that are passed in

dataset_column_dataprovider(*args, **kwargs)

Attempts to get column settings from dataset.metadata

dict_dataprovider(*args, **kwargs)

Uses column settings that are passed in

dataset_dict_dataprovider(*args, **kwargs)

Attempts to get column settings from dataset.metadata

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'column': <function column_dataprovider at 0x7fbb50a72320>, 'dataset-column': <function dataset_column_dataprovider at 0x7fbb50a72488>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7fbb50a72758>, 'dict': <function dict_dataprovider at 0x7fbb50a725f0>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.tabular.Tabular(**kwd)

Bases: galaxy.datatypes.tabular.TabularData

Tab delimited data

set_meta(dataset, overwrite=True, skip=None, max_data_lines=100000, max_guess_type_data_lines=None, **kwd)

Tries to determine the number of columns as well as those columns that contain numerical values in the dataset. A skip parameter is used because various tabular data types reuse this function, and their data type classes are responsible to determine how many invalid comment lines should be skipped. Using None for skip will cause skip to be zero, but the first line will be processed as a header. A max_data_lines parameter is used because various tabular data types reuse this function, and their data type classes are responsible to determine how many data lines should be processed to ensure that the non-optional metadata parameters are properly set; if used, optional metadata parameters will be set to None, unless the entire file has already been read. Using None for max_data_lines will process all data lines.

Items of interest:

1. We treat ‘overwrite’ as always True (we always want to set tabular metadata when called).
2. If a tabular file has no data, it will have one column of type ‘str’.
3. We used to check only the first 100 lines when setting metadata and this class’s set_peek() method read the entire file to determine the number of lines in the file. Since metadata can now be processed on cluster nodes, we’ve merged the line count portion of the set_peek() processing here, and we now check the entire contents of the file.

as_gbrowse_display_file(dataset, **kwd)

as_ucsc_display_file(dataset, **kwd)

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'column': <function column_dataprovider at 0x7fbb50a72320>, 'dataset-column': <function dataset_column_dataprovider at 0x7fbb50a72488>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7fbb50a72758>, 'dict': <function dict_dataprovider at 0x7fbb50a725f0>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.tabular.Taxonomy(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

__init__(**kwd)

Initialize taxonomy datatype

display_peek(dataset)

Returns formated html of peek

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.tabular.Sam(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

edam_format = 'format_2573'

edam_data = 'data_0863'

file_ext = 'sam'

track_type = 'ReadTrack'

data_sources = {'data': 'bam', 'index': 'bigwig'}

__init__(**kwd)

Initialize sam datatype

display_peek(dataset)

Returns formated html of peek

sniff_prefix(file_prefix)

Determines whether the file is in SAM format

A file in SAM format consists of lines of tab-separated data. The following header line may be the first line:

@QNAME  FLAG    RNAME   POS     MAPQ    CIGAR   MRNM    MPOS    ISIZE   SEQ     QUAL
or
@QNAME  FLAG    RNAME   POS     MAPQ    CIGAR   MRNM    MPOS    ISIZE   SEQ     QUAL    OPT

Data in the OPT column is optional and can consist of tab-separated data

For complete details see http://samtools.sourceforge.net/SAM1.pdf

Rules for sniffing as True:

There must be 11 or more columns of data on each line
Columns 2 (FLAG), 4(POS), 5 (MAPQ), 8 (MPOS), and 9 (ISIZE) must be numbers (9 can be negative)
We will only check that up to the first 5 alignments are correctly formatted.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'sequence.maf' )
>>> Sam().sniff( fname )
False
>>> fname = get_test_fname( '1.sam' )
>>> Sam().sniff( fname )
True

set_meta(dataset, overwrite=True, skip=None, max_data_lines=5, **kwd)

static merge(split_files, output_file)

Multiple SAM files may each have headers. Since the headers should all be the same, remove the headers from files 1-n, keeping them in the first file only

line_dataprovider(*args, **kwargs)

regex_line_dataprovider(*args, **kwargs)

column_dataprovider(*args, **kwargs)

dataset_column_dataprovider(*args, **kwargs)

dict_dataprovider(*args, **kwargs)

dataset_dict_dataprovider(*args, **kwargs)

header_dataprovider(*args, **kwargs)

id_seq_qual_dataprovider(*args, **kwargs)

genomic_region_dataprovider(*args, **kwargs)

genomic_region_dict_dataprovider(*args, **kwargs)

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'column': <function column_dataprovider at 0x7fbb50910500>, 'dataset-column': <function dataset_column_dataprovider at 0x7fbb50910668>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7fbb50910938>, 'dict': <function dict_dataprovider at 0x7fbb509107d0>, 'genomic-region': <function genomic_region_dataprovider at 0x7fbb50910d70>, 'genomic-region-dict': <function genomic_region_dict_dataprovider at 0x7fbb50910ed8>, 'header': <function header_dataprovider at 0x7fbb50910aa0>, 'id-seq-qual': <function id_seq_qual_dataprovider at 0x7fbb50910c08>, 'line': <function line_dataprovider at 0x7fbb50910230>, 'regex-line': <function regex_line_dataprovider at 0x7fbb50910398>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

sniff(filename)

class galaxy.datatypes.tabular.Pileup(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

Tab delimited data in pileup (6- or 10-column) format

edam_format = 'format_3015'

file_ext = 'pileup'

line_class = 'genomic coordinate'

data_sources = {'data': 'tabix'}

Add metadata elements

init_meta(dataset, copy_from=None)

display_peek(dataset)

Returns formated html of peek

repair_methods(dataset)

Return options for removing errors along with a description

sniff_prefix(file_prefix)

Checks for ‘pileup-ness’

There are two main types of pileup: 6-column and 10-column. For both, the first three and last two columns are the same. We only check the first three to allow for some personalization of the format.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'interval.interval' )
>>> Pileup().sniff( fname )
False
>>> fname = get_test_fname( '6col.pileup' )
>>> Pileup().sniff( fname )
True
>>> fname = get_test_fname( '10col.pileup' )
>>> Pileup().sniff( fname )
True
>>> fname = get_test_fname( '1.xls' )
>>> Pileup().sniff( fname )
False
>>> fname = get_test_fname( '2.txt' )
>>> Pileup().sniff( fname )  # 2.txt
False
>>> fname = get_test_fname( '2.tabular' )
>>> Pileup().sniff( fname )
False

genomic_region_dataprovider(*args, **kwargs)

genomic_region_dict_dataprovider(*args, **kwargs)

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'column': <function column_dataprovider at 0x7fbb50a72320>, 'dataset-column': <function dataset_column_dataprovider at 0x7fbb50a72488>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7fbb50a72758>, 'dict': <function dict_dataprovider at 0x7fbb50a725f0>, 'genomic-region': <function genomic_region_dataprovider at 0x7fbb50916488>, 'genomic-region-dict': <function genomic_region_dict_dataprovider at 0x7fbb509165f0>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', chromCol (ColumnParameter): Chrom column, defaults to '1', startCol (ColumnParameter): Start column, defaults to '2', endCol (ColumnParameter): End column, defaults to '2', baseCol (ColumnParameter): Reference base column, defaults to '3'

sniff(filename)

class galaxy.datatypes.tabular.BaseVcf(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

Variant Call Format for describing SNPs and other simple genome variations.

edam_format = 'format_3016'

track_type = 'VariantTrack'

data_sources = {'data': 'tabix', 'index': 'bigwig'}

column_names = ['Chrom', 'Pos', 'ID', 'Ref', 'Alt', 'Qual', 'Filter', 'Info', 'Format', 'data']

sniff_prefix(file_prefix)

display_peek(dataset)

Returns formated html of peek

set_meta(dataset, **kwd)

static merge(split_files, output_file)

genomic_region_dataprovider(*args, **kwargs)

genomic_region_dict_dataprovider(*args, **kwargs)

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'column': <function column_dataprovider at 0x7fbb50a72320>, 'dataset-column': <function dataset_column_dataprovider at 0x7fbb50a72488>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7fbb50a72758>, 'dict': <function dict_dataprovider at 0x7fbb50a725f0>, 'genomic-region': <function genomic_region_dataprovider at 0x7fbb50916b18>, 'genomic-region-dict': <function genomic_region_dict_dataprovider at 0x7fbb50916c80>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '10', column_types (ColumnTypesParameter): Column types, defaults to '['str', 'int', 'str', 'str', 'str', 'int', 'str', 'list', 'str', 'str']', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', viz_filter_cols (ColumnParameter): Score column for visualization, defaults to '[5]', sample_names (MetadataParameter): Sample names, defaults to '[]'

sniff(filename)

class galaxy.datatypes.tabular.Vcf(**kwd)

Bases: galaxy.datatypes.tabular.BaseVcf

file_ext = 'vcf'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '10', column_types (ColumnTypesParameter): Column types, defaults to '['str', 'int', 'str', 'str', 'str', 'int', 'str', 'list', 'str', 'str']', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', viz_filter_cols (ColumnParameter): Score column for visualization, defaults to '[5]', sample_names (MetadataParameter): Sample names, defaults to '[]'

class galaxy.datatypes.tabular.VcfGz(**kwd)

Bases: galaxy.datatypes.tabular.BaseVcf, galaxy.datatypes.binary.Binary

file_ext = 'vcf_bgzip'

compressed = True

compressed_format = 'gzip'

set_meta(dataset, **kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '10', column_types (ColumnTypesParameter): Column types, defaults to '['str', 'int', 'str', 'str', 'str', 'int', 'str', 'list', 'str', 'str']', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', viz_filter_cols (ColumnParameter): Score column for visualization, defaults to '[5]', sample_names (MetadataParameter): Sample names, defaults to '[]', tabix_index (FileParameter): Vcf Index File, defaults to 'None'

class galaxy.datatypes.tabular.Eland(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

Support for the export.txt.gz file used by Illumina’s ELANDv2e aligner

compressed = True

compressed_format = 'gzip'

file_ext = '_export.txt.gz'

__init__(**kwd)

Initialize eland datatype

make_html_table(dataset, skipchars=None)

Create HTML table, used for displaying peek

sniff_prefix(file_prefix)

Determines whether the file is in ELAND export format

A file in ELAND export format consists of lines of tab-separated data. There is no header.

Rules for sniffing as True:

- There must be 22 columns on each line
- LANE, TILEm X, Y, INDEX, READ_NO, SEQ, QUAL, POSITION, *STRAND, FILT must be correct
- We will only check that up to the first 5 alignments are correctly formatted.

set_meta(dataset, overwrite=True, skip=None, max_data_lines=5, **kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comments, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' ', tiles (ListParameter): Set of tiles, defaults to '[]', reads (ListParameter): Set of reads, defaults to '[]', lanes (ListParameter): Set of lanes, defaults to '[]', barcodes (ListParameter): Set of barcodes, defaults to '[]'

sniff(filename)

class galaxy.datatypes.tabular.ElandMulti(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

file_ext = 'elandmulti'

sniff_prefix(file_prefix)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

sniff(filename)

class galaxy.datatypes.tabular.FeatureLocationIndex(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

An index that stores feature locations in tabular format.

file_ext = 'fli'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '2', column_types (ColumnTypesParameter): Column types, defaults to '['str', 'str']', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.tabular.BaseCSV(**kwd)

Bases: galaxy.datatypes.tabular.TabularData

Delimiter-separated table data. This includes CSV, TSV and other dialects understood by the Python ‘csv’ module https://docs.python.org/2/library/csv.html Must be extended to define the dialect to use, strict_width and file_ext. See the Python module csv for documentation of dialect settings

delimiter = ','

peek_size = 1024

big_peek_size = 10240

is_int(column_text)

is_float(column_text)

guess_type(text)

sniff(filename)

Return True if if recognizes dialect and header.

set_meta(dataset, **kwd)

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'column': <function column_dataprovider at 0x7fbb50a72320>, 'dataset-column': <function dataset_column_dataprovider at 0x7fbb50a72488>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7fbb50a72758>, 'dict': <function dict_dataprovider at 0x7fbb50a725f0>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.tabular.CSV(**kwd)

Bases: galaxy.datatypes.tabular.BaseCSV

Comma-separated table data. Only sniffs comma-separated files with at least 2 rows and 2 columns.

file_ext = 'csv'

dialect

alias of csv.excel

strict_width = False

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'column': <function column_dataprovider at 0x7fbb50a72320>, 'dataset-column': <function dataset_column_dataprovider at 0x7fbb50a72488>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7fbb50a72758>, 'dict': <function dict_dataprovider at 0x7fbb50a725f0>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.tabular.TSV(**kwd)

Bases: galaxy.datatypes.tabular.BaseCSV

Tab-separated table data. Only sniff tab-separated files with at least 2 rows and 2 columns.

Note: Use of this datatype is optional as the general tabular datatype will handle most tab-separated files. This datatype is only required for datasets with tabs INSIDE double quotes.

This datatype currently does not support TSV files where the header has one column less to indicate first column is row names. This kind of file is handled fine by the tabular datatype.

file_ext = 'tsv'

dialect

alias of csv.excel_tab

strict_width = True

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'column': <function column_dataprovider at 0x7fbb50a72320>, 'dataset-column': <function dataset_column_dataprovider at 0x7fbb50a72488>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7fbb50a72758>, 'dict': <function dict_dataprovider at 0x7fbb50a725f0>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

class galaxy.datatypes.tabular.ConnectivityTable(**kwd)

Bases: galaxy.datatypes.tabular.Tabular

edam_format = 'format_3309'

file_ext = 'ct'

header_regexp = <_sre.SRE_Pattern object>

structure_regexp = <_sre.SRE_Pattern object>

__init__(**kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0', column_types (ColumnTypesParameter): Column types, defaults to '[]', column_names (MetadataParameter): Column names, defaults to '[]', delimiter (MetadataParameter): Data delimiter, defaults to ' '

set_meta(dataset, **kwd)

sniff(filename)

sniff_prefix(file_prefix)

The ConnectivityTable (CT) is a file format used for describing RNA 2D structures by tools including MFOLD, UNAFOLD and the RNAStructure package. The tabular file format is defined as follows:

5   energy = -12.3  sequence name
1   G       0       2       0       1
2   A       1       3       0       2
3   A       2       4       0       3
4   A       3       5       0       4
5   C       4       6       1       5

The links given at the edam ontology page do not indicate what type of separator is used (space or tab) while different implementations exist. The implementation that uses spaces as separator (implemented in RNAStructure) is as follows:

10    ENERGY = -34.8  seqname
1 G       0    2    9    1
2 G       1    3    8    2
3 G       2    4    7    3
4 a       3    5    0    4
5 a       4    6    0    5
6 a       5    7    0    6
7 C       6    8    3    7
8 C       7    9    2    8
9 C       8   10    1    9
10 a       9    0    0   10

get_chunk(trans, dataset, chunk)

galaxy.datatypes.text module

Clearing house for generic text datatypes that are not XML or tabular.

class galaxy.datatypes.text.Html(**kwd)

Bases: galaxy.datatypes.data.Text

Class describing an html file

edam_format = 'format_2331'

file_ext = 'html'

set_peek(dataset, is_multi_byte=False)

get_mime()

Returns the mime type of the datatype

sniff_prefix(file_prefix)

Determines whether the file is in html format

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'complete.bed' )
>>> Html().sniff( fname )
False
>>> fname = get_test_fname( 'file.html' )
>>> Html().sniff( fname )
True

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.text.Json(**kwd)

Bases: galaxy.datatypes.data.Text

edam_format = 'format_3464'

file_ext = 'json'

set_peek(dataset, is_multi_byte=False)

get_mime()

Returns the mime type of the datatype

sniff_prefix(file_prefix)

Try to load the string with the json module. If successful it’s a json file.

display_peek(dataset)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.text.Ipynb(**kwd)

Bases: galaxy.datatypes.text.Json

file_ext = 'ipynb'

set_peek(dataset, is_multi_byte=False)

sniff_prefix(file_prefix)

Try to load the string with the json module. If successful it’s a json file.

display_data(trans, dataset, preview=False, filename=None, to_ext=None, **kwd)

set_meta(dataset, **kwd)

Set the number of models in dataset.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.text.Biom1(**kwd)

Bases: galaxy.datatypes.text.Json

BIOM version 1.0 file format description http://biom-format.org/documentation/format_versions/biom-1.0.html

file_ext = 'biom1'

edam_format = 'format_3746'

set_peek(dataset, is_multi_byte=False)

sniff_prefix(file_prefix)

set_meta(dataset, **kwd)

Store metadata information from the BIOM file.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', table_rows (MetadataParameter): table_rows, defaults to '[]', table_matrix_element_type (MetadataParameter): table_matrix_element_type, defaults to '', table_format (MetadataParameter): table_format, defaults to '', table_generated_by (MetadataParameter): table_generated_by, defaults to '', table_matrix_type (MetadataParameter): table_matrix_type, defaults to '', table_shape (MetadataParameter): table_shape, defaults to '[]', table_format_url (MetadataParameter): table_format_url, defaults to '', table_date (MetadataParameter): table_date, defaults to '', table_type (MetadataParameter): table_type, defaults to '', table_id (MetadataParameter): table_id, defaults to 'None', table_columns (MetadataParameter): table_columns, defaults to '[]'

sniff(filename)

class galaxy.datatypes.text.Obo(**kwd)

Bases: galaxy.datatypes.data.Text

OBO file format description https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html

edam_data = 'data_0582'

edam_format = 'format_2549'

file_ext = 'obo'

set_peek(dataset, is_multi_byte=False)

sniff_prefix(file_prefix)

Try to guess the Obo filetype. It usually starts with a “format-version:” string and has several stanzas which starts with “id:”.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.text.Arff(**kwd)

Bases: galaxy.datatypes.data.Text

An ARFF (Attribute-Relation File Format) file is an ASCII text file that describes a list of instances sharing a set of attributes. http://weka.wikispaces.com/ARFF

edam_format = 'format_3581'

file_ext = 'arff'

Add metadata elements

set_peek(dataset, is_multi_byte=False)

sniff_prefix(file_prefix)

Try to guess the Arff filetype. It usually starts with a “format-version:” string and has several stanzas which starts with “id:”.

set_meta(dataset, **kwd)

Trying to count the comment lines and the number of columns included. A typical ARFF data block looks like this: @DATA 5.1,3.5,1.4,0.2,Iris-setosa 4.9,3.0,1.4,0.2,Iris-setosa

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', comment_lines (MetadataParameter): Number of comment lines, defaults to '0', columns (MetadataParameter): Number of columns, defaults to '0'

sniff(filename)

class galaxy.datatypes.text.SnpEffDb(**kwd)

Bases: galaxy.datatypes.data.Text

Class describing a SnpEff genome build

edam_format = 'format_3624'

file_ext = 'snpeffdb'

__init__(**kwd)

getSnpeffVersionFromFile(path)

set_meta(dataset, **kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', genome_version (MetadataParameter): Genome Version, defaults to 'None', snpeff_version (MetadataParameter): SnpEff Version, defaults to 'SnpEff4.0', regulation (MetadataParameter): Regulation Names, defaults to '[]', annotation (MetadataParameter): Annotation Names, defaults to '[]'

class galaxy.datatypes.text.SnpSiftDbNSFP(**kwd)

Bases: galaxy.datatypes.data.Text

Class describing a dbNSFP database prepared fpr use by SnpSift dbnsfp

file_ext = 'snpsiftdbnsfp'

composite_type = 'auto_primary_file'

allow_datatype_change = False

## The dbNSFP file is a tabular file with 1 header line ## The first 4 columns are required to be: chrom pos ref alt ## These match columns 1,2,4,5 of the VCF file ## SnpSift requires the file to be block-gzipped and the indexed with samtools tabix ## Example: ## Compress using block-gzip algorithm bgzip dbNSFP2.3.txt ## Create tabix index tabix -s 1 -b 2 -e 2 dbNSFP2.3.txt.gz

__init__(**kwd)

init_meta(dataset, copy_from=None)

generate_primary_file(dataset=None)

This is called only at upload to write the html file cannot rename the datasets here - they come with the default unfortunately

regenerate_primary_file(dataset)

cannot do this until we are setting metadata

set_meta(dataset, overwrite=True, **kwd)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0', reference_name (MetadataParameter): Reference Name, defaults to 'dbSNFP', bgzip (MetadataParameter): dbNSFP bgzip, defaults to 'None', index (MetadataParameter): Tabix Index File, defaults to 'None', annotation (MetadataParameter): Annotation Names, defaults to '[]'

class galaxy.datatypes.text.IQTree(**kwd)

Bases: galaxy.datatypes.data.Text

IQ-TREE format

file_ext = 'iqtree'

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

sniff_prefix(file_prefix)

Detect the IQTree file

Scattered text file containing various headers and data types.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('example.iqtree')
>>> IQTree().sniff(fname)
True

>>> fname = get_test_fname('temp.txt')
>>> IQTree().sniff(fname)
False

>>> fname = get_test_fname('test_tab1.tabular')
>>> IQTree().sniff(fname)
False

galaxy.datatypes.tracks module

Datatype classes for tracks/track views within galaxy.

class galaxy.datatypes.tracks.GeneTrack(**kwargs)

Bases: galaxy.datatypes.binary.Binary

edam_data = 'data_3002'

edam_format = 'format_2919'

file_ext = 'genetrack'

__init__(**kwargs)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.tracks.UCSCTrackHub(**kwd)

Bases: galaxy.datatypes.text.Html

Datatype for UCSC TrackHub

file_ext = 'trackhub'

composite_type = 'auto_primary_file'

__init__(**kwd)

generate_primary_file(dataset=None)

This is called only at upload to write the html file cannot rename the datasets here - they come with the default unfortunately

set_peek(dataset, is_multi_byte=False)

display_peek(dataset)

sniff(filename)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

galaxy.datatypes.triples module

Triple format classes

class galaxy.datatypes.triples.Triples(**kwd)

Bases: galaxy.datatypes.data.Data

The abstract base class for the file format that can contain triples

edam_data = 'data_0582'

edam_format = 'format_2376'

file_ext = 'triples'

sniff(filename)

Returns false and the user must manually set.

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

class galaxy.datatypes.triples.NTriples(**kwd)

Bases: galaxy.datatypes.data.Text, galaxy.datatypes.triples.Triples

The N-Triples triple data format

edam_format = 'format_3256'

file_ext = 'nt'

sniff_prefix(file_prefix)

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.triples.N3(**kwd)

Bases: galaxy.datatypes.data.Text, galaxy.datatypes.triples.Triples

The N3 triple data format

edam_format = 'format_3257'

file_ext = 'n3'

sniff(filename)

Returns false and the user must manually set.

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.triples.Turtle(**kwd)

Bases: galaxy.datatypes.data.Text, galaxy.datatypes.triples.Triples

The Turtle triple data format

edam_format = 'format_3255'

file_ext = 'ttl'

sniff_prefix(file_prefix)

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.triples.Rdf(**kwd)

Bases: galaxy.datatypes.xml.GenericXml, galaxy.datatypes.triples.Triples

Resource Description Framework format (http://www.w3.org/RDF/).

edam_format = 'format_3261'

file_ext = 'rdf'

sniff_prefix(file_prefix)

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.triples.Jsonld(**kwd)

Bases: galaxy.datatypes.text.Json, galaxy.datatypes.triples.Triples

The JSON-LD data format

edam_format = 'format_3464'

file_ext = 'jsonld'

sniff_prefix(file_prefix)

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.triples.HDT(**kwd)

Bases: galaxy.datatypes.binary.Binary, galaxy.datatypes.triples.Triples

The HDT triple data format

edam_format = 'format_2376'

file_ext = 'hdt'

sniff(filename)

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?'

galaxy.datatypes.upload_util module

exception galaxy.datatypes.upload_util.UploadProblemException(message)

Bases: exceptions.Exception

__init__(message)

galaxy.datatypes.upload_util.handle_upload(registry, path, requested_ext, name, tmp_prefix, tmp_dir, check_content, link_data_only, in_place, auto_decompress, convert_to_posix_lines, convert_spaces_to_tabs)

galaxy.datatypes.xml module

XML format classes

class galaxy.datatypes.xml.GenericXml(**kwd)

Bases: galaxy.datatypes.data.Text

Base format class for any XML file.

edam_format = 'format_2332'

file_ext = 'xml'

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

sniff_prefix(file_prefix)

Determines whether the file is XML or not

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' )
>>> GenericXml().sniff( fname )
True
>>> fname = get_test_fname( 'interval.interval' )
>>> GenericXml().sniff( fname )
False

static merge(split_files, output_file)

Merging multiple XML files is non-trivial and must be done in subclasses.

xml_dataprovider(*args, **kwargs)

dataproviders = {'base': <function base_dataprovider at 0x7fbb506af848>, 'chunk': <function chunk_dataprovider at 0x7fbb506af9b0>, 'chunk64': <function chunk64_dataprovider at 0x7fbb506afb18>, 'line': <function line_dataprovider at 0x7fbb506b5140>, 'regex-line': <function regex_line_dataprovider at 0x7fbb506b52a8>, 'xml': <function xml_dataprovider at 0x7fbb327fc2a8>}

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

class galaxy.datatypes.xml.MEMEXml(**kwd)

Bases: galaxy.datatypes.xml.GenericXml

MEME XML Output data

file_ext = 'memexml'

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

sniff_prefix(file_prefix)

class galaxy.datatypes.xml.CisML(**kwd)

Bases: galaxy.datatypes.xml.GenericXml

CisML XML data

file_ext = 'cisml'

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff(filename)

sniff_prefix(file_prefix)

class galaxy.datatypes.xml.Phyloxml(**kwd)

Bases: galaxy.datatypes.xml.GenericXml

Format for defining phyloxml data http://www.phyloxml.org/

edam_data = 'data_0872'

edam_format = 'format_3159'

file_ext = 'phyloxml'

set_peek(dataset, is_multi_byte=False)

Set the peek and blurb text

sniff_prefix(file_prefix)

“Checking for keyword - ‘phyloxml’ always in lowercase in the first few lines.

>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname( '1.phyloxml' )
>>> Phyloxml().sniff( fname )
True
>>> fname = get_test_fname( 'interval.interval' )
>>> Phyloxml().sniff( fname )
False
>>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' )
>>> Phyloxml().sniff( fname )
False

get_visualizations(dataset)

Returns a list of visualizations for datatype.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.xml.Owl(**kwd)

Bases: galaxy.datatypes.xml.GenericXml

Web Ontology Language OWL format description http://www.w3.org/TR/owl-ref/

edam_format = 'format_3262'

file_ext = 'owl'

set_peek(dataset, is_multi_byte=False)

sniff_prefix(file_prefix)

Checking for keyword - ‘<owl’ in the first 200 lines.

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

class galaxy.datatypes.xml.Sbml(**kwd)

Bases: galaxy.datatypes.xml.GenericXml

System Biology Markup Language http://sbml.org

file_ext = 'sbml'

edam_data = 'data_2024'

edam_format = 'format_2585'

set_peek(dataset, is_multi_byte=False)

metadata_spec = dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'

sniff_prefix(file_prefix)

Checking for keyword - ‘<sbml’ in the first 200 lines.