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galaxy.datatypes package¶
Subpackages¶
- galaxy.datatypes.converters package
- Submodules
- galaxy.datatypes.converters.bcf_bgzip_to_bcf_converter module
- galaxy.datatypes.converters.bcf_to_bcf_bgzip_converter module
- 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.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
- galaxy.datatypes.util package
Submodules¶
galaxy.datatypes.assembly module¶
velvet datatypes James E Johnson - University of Minnesota for velvet assembler tool in galaxy
-
class
galaxy.datatypes.assembly.
Amos
(**kwd)[source]¶ 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)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.sequence.Fasta
Class describing the Sequences file generated by velveth
-
edam_data
= 'data_0925'¶
-
file_ext
= 'sequences'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.data.Text
Class describing the Sequences file generated by velveth
-
edam_format
= 'format_2561'¶
-
file_ext
= 'roadmaps'¶
-
sniff_prefix
(file_prefix)[source]¶ - 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)[source]¶ Bases:
galaxy.datatypes.text.Html
-
composite_type
= 'auto_primary_file'¶
-
allow_datatype_change
= False¶
-
file_ext
= 'velvet'¶
-
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)[source]¶ Bases:
galaxy.datatypes.data.Data
Binary data
-
edam_format
= 'format_2333'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
Ab1
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class describing an ab1 binary sequence file
-
file_ext
= 'ab1'¶
-
edam_format
= 'format_3000'¶
-
edam_data
= 'data_0924'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
Idat
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Binary data in idat format
-
file_ext
= 'idat'¶
-
edam_format
= 'format_2058'¶
-
edam_data
= 'data_2603'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
Cel
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Binary data in CEL format.
-
file_ext
= 'cel'¶
-
edam_format
= 'format_1638'¶
-
edam_data
= 'data_3110'¶
-
sniff
(filename)[source]¶ 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)[source]¶ 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¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
DynamicCompressedArchive
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.CompressedArchive
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
GzDynamicCompressedArchive
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.DynamicCompressedArchive
-
compressed_format
= 'gzip'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
Bz2DynamicCompressedArchive
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.DynamicCompressedArchive
-
compressed_format
= 'bz2'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
CompressedZipArchive
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
GenericAsn1Binary
(**kwd)[source]¶ 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)[source]¶ 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)[source]¶ Merges BAM files
Parameters: - split_files – List of bam file paths to merge
- output_file – Write merged bam file to this location
-
groom_dataset_content
(file_name)[source]¶ Ensures that the BAM file contents are coordinate-sorted. This function is called on an output dataset after the content is initially generated.
-
display_data
(trans, dataset, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd)[source]¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', bam_index (FileParameter): BAM Index File, defaults to 'None', 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)[source]¶ 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)[source]¶ Check if file_name is a coordinate-sorted BAM file
-
samtools_dataprovider
(*args, **kwargs)[source]¶ Generic samtools interface - all options available through settings.
-
dataproviders
= {'base': <function base_dataprovider at 0x7f6a67013320>, 'chunk': <function chunk_dataprovider at 0x7f6a67013488>, 'chunk64': <function chunk64_dataprovider at 0x7f6a670135f0>, 'column': <function column_dataprovider at 0x7f6a67012b18>, 'dict': <function dict_dataprovider at 0x7f6a67012c80>, 'genomic-region': <function genomic_region_dataprovider at 0x7f6a6701c140>, 'genomic-region-dict': <function genomic_region_dict_dataprovider at 0x7f6a6701c2a8>, 'header': <function header_dataprovider at 0x7f6a67012de8>, 'id-seq-qual': <function id_seq_qual_dataprovider at 0x7f6a67012f50>, 'line': <function line_dataprovider at 0x7f6a67012848>, 'regex-line': <function regex_line_dataprovider at 0x7f6a670129b0>, 'samtools': <function samtools_dataprovider at 0x7f6a6701c410>}¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', bam_index (FileParameter): BAM Index File, defaults to 'None', 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.
ProBam
(**kwd)[source]¶ 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_index (FileParameter): BAM Index File, defaults to 'None', 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.
BamInputSorted
(**kwd)[source]¶ 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.
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', bam_index (FileParameter): BAM Index File, defaults to 'None', 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)[source]¶ Bases:
galaxy.datatypes.binary.BamInputSorted
A class for queryname sorted BAM files.
-
sort_flag
= '-n'¶
-
file_ext
= 'qname_sorted.bam'¶
-
dataset_content_needs_grooming
(file_name)[source]¶ Check if file_name is a queryname-sorted BAM file
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', bam_index (FileParameter): BAM Index File, defaults to 'None', 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)[source]¶ Bases:
galaxy.datatypes.binary.Binary
-
file_ext
= 'cram'¶
-
edam_format
= 'format_3462'¶
-
edam_data
= 'format_0863'¶
-
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)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.binary.BaseBcf
Class describing a (BGZF-compressed) BCF file
-
file_ext
= 'bcf'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', bcf_index (FileParameter): BCF Index File, defaults to 'None'¶
-
-
class
galaxy.datatypes.binary.
BcfUncompressed
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', bcf_index (FileParameter): BCF Index File, defaults to 'None'¶
-
-
class
galaxy.datatypes.binary.
H5
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
Biom2
(**kwd)[source]¶ 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)[source]¶ >>> 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
-
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)[source]¶ Bases:
galaxy.datatypes.binary.H5
Class describing the cool format (https://github.com/mirnylab/cooler)
-
file_ext
= 'cool'¶
-
sniff
(filename)[source]¶ >>> 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
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
Scf
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class describing an scf binary sequence file
-
edam_format
= 'format_1632'¶
-
edam_data
= 'data_0924'¶
-
file_ext
= 'scf'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
Sff
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Standard Flowgram Format (SFF)
-
edam_format
= 'format_3284'¶
-
edam_data
= 'data_0924'¶
-
file_ext
= 'sff'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
BigWig
(**kwd)[source]¶ 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'}¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
BigBed
(**kwd)[source]¶ 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'}¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
TwoBit
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class describing a TwoBit format nucleotide file
-
edam_format
= 'format_3009'¶
-
edam_data
= 'data_0848'¶
-
file_ext
= 'twobit'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
SQlite
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class describing a Sqlite database
-
file_ext
= 'sqlite'¶
-
edam_format
= 'format_3621'¶
-
dataproviders
= {'base': <function base_dataprovider at 0x7f6a67013320>, 'chunk': <function chunk_dataprovider at 0x7f6a67013488>, 'chunk64': <function chunk64_dataprovider at 0x7f6a670135f0>, 'sqlite': <function sqlite_dataprovider at 0x7f6a832e00c8>, 'sqlite-dict': <function sqlite_datadictprovider at 0x7f6a832e0398>, 'sqlite-table': <function sqlite_datatableprovider at 0x7f6a832e0230>}¶
-
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)[source]¶ Bases:
galaxy.datatypes.binary.SQlite
Class describing a Gemini Sqlite database
-
file_ext
= 'gemini.sqlite'¶
-
edam_format
= 'format_3622'¶
-
edam_data
= 'data_3498'¶
-
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.
MzSQlite
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.SQlite
Class describing a Proteomics Sqlite database
-
file_ext
= 'mz.sqlite'¶
-
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.
IdpDB
(**kwd)[source]¶ 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'¶
-
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.
Xlsx
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class for Excel 2007 (xlsx) files
-
file_ext
= 'xlsx'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
ExcelXls
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class describing an Excel (xls) file
-
file_ext
= 'excel.xls'¶
-
edam_format
= 'format_3468'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
Sra
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Sequence Read Archive (SRA) datatype originally from mdshw5/sra-tools-galaxy
-
file_ext
= 'sra'¶
-
sniff
(filename)[source]¶ 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
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
RData
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Generic R Data file datatype implementation
-
file_ext
= 'rdata'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
OxliBinary
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
OxliCountGraph
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
OxliNodeGraph
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
OxliTagSet
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
OxliStopTags
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
OxliSubset
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
OxliGraphLabels
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
PostgresqlArchive
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', version (MetadataParameter): PostgreSQL database version, defaults to 'None'¶
-
-
class
galaxy.datatypes.binary.
Fast5Archive
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', fast5_count (MetadataParameter): Read Count, defaults to '0'¶
-
-
class
galaxy.datatypes.binary.
Fast5ArchiveGz
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', fast5_count (MetadataParameter): Read Count, defaults to '0'¶
-
-
class
galaxy.datatypes.binary.
Fast5ArchiveBz2
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', fast5_count (MetadataParameter): Read Count, defaults to '0'¶
-
-
class
galaxy.datatypes.binary.
SearchGuiArchive
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.CompressedArchive
Class describing a SearchGUI archive
-
file_ext
= 'searchgui_archive'¶
-
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)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Binary data in netCDF format
-
file_ext
= 'netcdf'¶
-
edam_format
= 'format_3650'¶
-
edam_data
= 'data_0943'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.binary.
DMND
(**kwd)[source]¶ 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'¶
-
edam_format
= ''¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
galaxy.datatypes.blast module¶
NCBI BLAST datatypes.
Covers the blastxml
format and the BLAST databases.
-
class
galaxy.datatypes.blast.
BlastXml
(**kwd)[source]¶ Bases:
galaxy.datatypes.xml.GenericXml
NCBI Blast XML Output data
-
file_ext
= 'blastxml'¶
-
edam_format
= 'format_3331'¶
-
edam_data
= 'data_0857'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ 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)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.blast.
BlastProtDb
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.blast.
BlastDomainDb
(**kwd)[source]¶ 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'¶
-
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.chrominfo module¶
-
class
galaxy.datatypes.chrominfo.
ChromInfo
(**kwd)[source]¶ 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)[source]¶ 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
= ''¶
-
sniff_prefix
(file_prefix)[source]¶ The structure of a typical PLY file: Header, Vertex List, Face List, (lists of other elements)
-
sniff
(filename)¶
-
-
class
galaxy.datatypes.constructive_solid_geometry.
PlyAscii
(**kwd)[source]¶ Bases:
galaxy.datatypes.constructive_solid_geometry.Ply
,galaxy.datatypes.data.Text
-
file_ext
= 'plyascii'¶
-
subtype
= 'ascii'¶
-
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)[source]¶ Bases:
galaxy.datatypes.constructive_solid_geometry.Ply
,galaxy.datatypes.binary.Binary
-
file_ext
= 'plybinary'¶
-
subtype
= 'binary'¶
-
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)[source]¶ 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
= ''¶
-
sniff_prefix
(file_prefix)[source]¶ 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_structure_metadata
(line, dataset, dataset_type)[source]¶ 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.
-
sniff
(filename)¶
-
-
class
galaxy.datatypes.constructive_solid_geometry.
VtkAscii
(**kwd)[source]¶ Bases:
galaxy.datatypes.constructive_solid_geometry.Vtk
,galaxy.datatypes.data.Text
-
file_ext
= 'vtkascii'¶
-
subtype
= 'ASCII'¶
-
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)[source]¶ Bases:
galaxy.datatypes.constructive_solid_geometry.Vtk
,galaxy.datatypes.binary.Binary
-
file_ext
= 'vtkbinary'¶
-
subtype
= 'BINARY'¶
-
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)[source]¶ Bases:
galaxy.datatypes.data.Data
-
file_ext
= 'stl'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
galaxy.datatypes.coverage module¶
Coverage datatypes
-
class
galaxy.datatypes.coverage.
LastzCoverage
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'coverage'¶
-
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_)[source]¶ Bases:
abc.ABCMeta
Metaclass for Data class. Sets up metadata spec.
-
class
galaxy.datatypes.data.
Data
(**kwd)[source]¶ 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'>
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edam_data
= 'data_0006'¶
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edam_format
= 'format_1915'¶
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file_ext
= 'data'¶
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CHUNKABLE
= False¶
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metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶ Dictionary of metadata fields for this datatype
-
copy_safe_peek
= True¶
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is_binary
= True¶
-
allow_datatype_change
= True¶
-
composite_type
= None¶
-
primary_file_name
= 'index'¶
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track_type
= None¶
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data_sources
= {}¶
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supported_display_apps
= {}¶
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composite_files
= {}¶
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get_raw_data
(dataset)[source]¶ Returns the full data. To stream it open the file_name and read/write as needed
-
dataset_content_needs_grooming
(file_name)[source]¶ This function is called on an output dataset file after the content is initially generated.
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groom_dataset_content
(file_name)[source]¶ This function is called on an output dataset file if dataset_content_needs_grooming returns True.
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set_meta
(dataset, overwrite=True, **kwd)[source]¶ Unimplemented method, allows guessing of metadata from contents of file
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missing_meta
(dataset, check=[], skip=[])[source]¶ 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
-
max_optional_metadata_filesize
¶
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set_peek
(dataset, is_multi_byte=False)[source]¶ Set the peek and blurb text
Parameters: is_multi_byte (bool) – deprecated
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to_archive
(trans, dataset, name='')[source]¶ 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’
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display_data
(trans, data, preview=False, filename=None, to_ext=None, **kwd)[source]¶ Old display method, for transition - though still used by API and test framework. 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?).
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repair_methods
(dataset)[source]¶ Unimplemented method, returns dict with method/option for repairing errors
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add_display_app
(app_id, label, file_function, links_function)[source]¶ 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)
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as_display_type
(dataset, type, **kwd)[source]¶ Returns modified file contents for a particular display type
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get_display_links
(dataset, type, app, base_url, target_frame='_blank', **kwd)[source]¶ 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.
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get_converter_types
(original_dataset, datatypes_registry)[source]¶ Returns available converters by type for this dataset
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find_conversion_destination
(dataset, accepted_formats, datatypes_registry, **kwd)[source]¶ Returns ( target_ext, existing converted dataset )
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convert_dataset
(trans, original_dataset, target_type, return_output=False, visible=True, deps=None, target_context=None, history=None)[source]¶ This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure.
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after_setting_metadata
(dataset)[source]¶ This function is called on the dataset after metadata is set.
-
before_setting_metadata
(dataset)[source]¶ This function is called on the dataset before metadata is set.
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writable_files
¶
-
has_resolution
¶
-
matches_any
(target_datatypes)[source]¶ Check if this datatype is of any of the target_datatypes or is a subtype thereof.
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static
merge
(split_files, output_file)[source]¶ Merge files with copy.copyfileobj() will not hit the max argument limitation of cat. gz and bz2 files are also working.
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dataprovider
(dataset, data_format, **settings)[source]¶ Base dataprovider factory for all datatypes that returns the proper provider for the given data_format or raises a NoProviderAvailable.
-
dataproviders
= {'base': <function base_dataprovider at 0x7f6a67013320>, 'chunk': <function chunk_dataprovider at 0x7f6a67013488>, 'chunk64': <function chunk64_dataprovider at 0x7f6a670135f0>}¶
-
-
class
galaxy.datatypes.data.
Text
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Data
-
edam_format
= 'format_2330'¶
-
file_ext
= 'txt'¶
-
line_class
= 'line'¶
-
is_binary
= False¶
-
estimate_file_lines
(dataset)[source]¶ Perform a rough estimate by extrapolating number of lines from a small read.
-
count_data_lines
(dataset)[source]¶ 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)[source]¶ Set the peek. This method is used by various subclasses of Text.
-
classmethod
split
(input_datasets, subdir_generator_function, split_params)[source]¶ Split the input files by line.
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line_dataprovider
(*args, **kwargs)[source]¶ Returns an iterator over the dataset’s lines (that have been stripped) optionally excluding blank lines and lines that start with a comment character.
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regex_line_dataprovider
(*args, **kwargs)[source]¶ 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 0x7f6a67013320>, 'chunk': <function chunk_dataprovider at 0x7f6a67013488>, 'chunk64': <function chunk64_dataprovider at 0x7f6a670135f0>, 'line': <function line_dataprovider at 0x7f6a67013b90>, 'regex-line': <function regex_line_dataprovider at 0x7f6a67013cf8>}¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
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-
class
galaxy.datatypes.data.
GenericAsn1
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
Class for generic ASN.1 text format
-
edam_data
= 'data_0849'¶
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edam_format
= 'format_1966'¶
-
file_ext
= 'asn1'¶
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metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
-
class
galaxy.datatypes.data.
LineCount
(**kwd)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.data.Text
New Hampshire/Newick Format
-
edam_data
= 'data_0872'¶
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edam_format
= 'format_1910'¶
-
file_ext
= 'nhx'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
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-
class
galaxy.datatypes.data.
Nexus
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
Nexus format as used By Paup, Mr Bayes, etc
-
edam_data
= 'data_0872'¶
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edam_format
= 'format_1912'¶
-
file_ext
= 'nex'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
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sniff
(filename)¶
-
-
galaxy.datatypes.data.
get_file_peek
(file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skipchars=None, line_wrap=True)[source]¶ Returns the first LINE_COUNT lines wrapped to WIDTH.
Parameters: is_multi_byte (bool) – deprecated >>> fname = get_test_fname('4.bed') >>> 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
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class
galaxy.datatypes.genetics.
GenomeGraphs
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
Tab delimited data containing a marker id and any number of numeric values
-
file_ext
= 'gg'¶
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ucsc_links
(dataset, type, app, base_url)[source]¶ 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
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sniff_prefix
(file_prefix)[source]¶ 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
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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)[source]¶ 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'¶
-
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)[source]¶ 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'¶
-
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)[source]¶ 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'¶
-
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 ' '¶
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-
class
galaxy.datatypes.genetics.
Rgenetics
(**kwd)[source]¶ 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'¶
-
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'¶
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-
class
galaxy.datatypes.genetics.
SNPMatrix
(**kwd)[source]¶ Bases:
galaxy.datatypes.genetics.Rgenetics
BioC SNPMatrix Rgenetics data collections
-
file_ext
= 'snpmatrix'¶
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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)[source]¶ Bases:
galaxy.datatypes.genetics.Rgenetics
linkage pedigree (ped,map) Rgenetics data collections
-
file_ext
= 'lped'¶
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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)[source]¶ Bases:
galaxy.datatypes.genetics.Rgenetics
Plink phenotype file - header must have FID IID… Rgenetics data collections
-
file_ext
= 'pphe'¶
-
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)[source]¶ Bases:
galaxy.datatypes.genetics.Rgenetics
fbat pedigree file - mad format with ! as first char on header row Rgenetics data collections
-
file_ext
= 'fphe'¶
-
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)[source]¶ Bases:
galaxy.datatypes.genetics.Rgenetics
Phenotype file
-
file_ext
= 'phe'¶
-
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)[source]¶ Bases:
galaxy.datatypes.genetics.Rgenetics
FBAT pedigree format - single file, map is header row of rs numbers. Strange. Rgenetics data collections
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file_ext
= 'fped'¶
-
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)[source]¶ Bases:
galaxy.datatypes.genetics.Rgenetics
Plink Binary compressed 2bit/geno Rgenetics data collections
-
file_ext
= 'pbed'¶
-
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)[source]¶ 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'¶
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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)[source]¶ 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'¶
-
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)[source]¶ Bases:
galaxy.datatypes.genetics.Rgenetics
Eigenstrat PCA file for case control adjustment Rgenetics data collections
-
file_ext
= 'eigenstratpca'¶
-
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)[source]¶ 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)[source]¶ 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'¶
-
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)[source]¶ 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)[source]¶ 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¶
-
generate_primary_file
(dataset=None)[source]¶ This is called only at upload to write the html file cannot rename the datasets here - they come with the default unfortunately
-
get_phecols
(phenolist=[], maxConc=20)[source]¶ 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 :)
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get_pheno
(dataset)[source]¶ 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)
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set_peek
(dataset, **kwd)[source]¶ 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_file_peek
(filename)[source]¶ can’t really peek at a filename - need the extra_files_path and such?
-
set_meta
(dataset, **kwd)[source]¶ 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')[source]¶ Create HTML table, used for displaying 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)[source]¶ Bases:
galaxy.datatypes.genetics.RexpBase
derived class for BioC data structures in Galaxy
-
file_ext
= 'affybatch'¶
-
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)[source]¶ Bases:
galaxy.datatypes.genetics.RexpBase
derived class for BioC data structures in Galaxy
-
file_ext
= 'eset'¶
-
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)[source]¶ Bases:
galaxy.datatypes.genetics.RexpBase
derived class for BioC data structures in Galaxy
-
file_ext
= 'malist'¶
-
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)[source]¶ 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']¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
-
class
galaxy.datatypes.genetics.
GenotypeMatrix
(**kwd)[source]¶ Bases:
galaxy.datatypes.genetics.LinkageStudies
Sample matrix of genotypes - GTs as columns
-
file_ext
= 'alohomora_gts'¶
-
sniff_prefix
(file_prefix)[source]¶ >>> 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)[source]¶ 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'¶
-
sniff_prefix
(file_prefix)[source]¶ >>> 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)[source]¶ Bases:
galaxy.datatypes.genetics.LinkageStudies
Common linkage input file for intermarker distances and recombination rates
-
file_ext
= 'linkage_datain'¶
-
sniff_prefix
(file_prefix)[source]¶ >>> 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)[source]¶ Bases:
galaxy.datatypes.genetics.LinkageStudies
Allegro output format for LOD scores
-
file_ext
= 'allegro_fparam'¶
-
sniff_prefix
(file_prefix)[source]¶ >>> 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)[source]¶ Bases:
galaxy.datatypes.xml.GenericXml
XGMML graph format (http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats).
-
file_ext
= 'xgmml'¶
-
static
merge
(split_files, output_file)[source]¶ Merging multiple XML files is non-trivial and must be done in subclasses.
-
dataproviders
= {'base': <function base_dataprovider at 0x7f6a67013320>, 'chunk': <function chunk_dataprovider at 0x7f6a67013488>, 'chunk64': <function chunk64_dataprovider at 0x7f6a670135f0>, 'line': <function line_dataprovider at 0x7f6a67013b90>, 'node-edge': <function node_edge_dataprovider at 0x7f6a5a2ddb90>, 'regex-line': <function regex_line_dataprovider at 0x7f6a67013cf8>, 'xml': <function xml_dataprovider at 0x7f6a644bf668>}¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
-
class
galaxy.datatypes.graph.
Sif
(**kwd)[source]¶ 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'¶
-
dataproviders
= {'base': <function base_dataprovider at 0x7f6a67013320>, 'chunk': <function chunk_dataprovider at 0x7f6a67013488>, 'chunk64': <function chunk64_dataprovider at 0x7f6a670135f0>, 'column': <function column_dataprovider at 0x7f6a832ce1b8>, 'dataset-column': <function dataset_column_dataprovider at 0x7f6a832ce320>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7f6a832ce5f0>, 'dict': <function dict_dataprovider at 0x7f6a832ce488>, 'line': <function line_dataprovider at 0x7f6a67013b90>, 'node-edge': <function node_edge_dataprovider at 0x7f6a5a1d6050>, 'regex-line': <function regex_line_dataprovider at 0x7f6a67013cf8>}¶
-
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)[source]¶ 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)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.data.Data
Class describing an image
-
edam_data
= 'data_2968'¶
-
edam_format
= 'format_3547'¶
-
file_ext
= ''¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.images.
Jpg
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3579'¶
-
file_ext
= 'jpg'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.images.
Png
(**kwd)[source]¶ 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)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.images.Image
-
file_ext
= 'vms'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.images.
Mirax
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
file_ext
= 'mrxs'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.images.
Sakura
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
file_ext
= 'svslide'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.images.
Nrrd
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
file_ext
= 'nrrd'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.images.
Bmp
(**kwd)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3508'¶
-
file_ext
= 'pdf'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.images.
Gmaj
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Data
Class describing a GMAJ Applet
-
edam_format
= 'format_3547'¶
-
file_ext
= 'gmaj.zip'¶
-
copy_safe_peek
= False¶
-
sniff
(filename)[source]¶ 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)[source]¶ 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'¶
-
galaxy.datatypes.interval module¶
Interval datatypes
-
class
galaxy.datatypes.interval.
Interval
(**kwd)[source]¶ 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
-
set_meta
(dataset, overwrite=True, first_line_is_header=False, **kwd)[source]¶ Tries to guess from the line the location number of the column for the chromosome, region start-end and strand
-
get_estimated_display_viewport
(dataset, chrom_col=None, start_col=None, end_col=None)[source]¶ Return a chrom, start, stop tuple for viewing a file.
-
ucsc_links
(dataset, type, app, base_url)[source]¶ Generate links to UCSC genome browser sites based on the dbkey and content of dataset.
-
sniff_prefix
(file_prefix)[source]¶ 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
-
dataproviders
= {'base': <function base_dataprovider at 0x7f6a67013320>, 'chunk': <function chunk_dataprovider at 0x7f6a67013488>, 'chunk64': <function chunk64_dataprovider at 0x7f6a670135f0>, 'column': <function column_dataprovider at 0x7f6a832ce1b8>, 'dataset-column': <function dataset_column_dataprovider at 0x7f6a832ce320>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7f6a832ce5f0>, 'dict': <function dict_dataprovider at 0x7f6a832ce488>, 'genomic-region': <function genomic_region_dataprovider at 0x7f6a84090398>, 'genomic-region-dict': <function genomic_region_dict_dataprovider at 0x7f6a84090500>, 'interval': <function interval_dataprovider at 0x7f6a84090668>, 'interval-dict': <function interval_dict_dataprovider at 0x7f6a840907d0>, 'line': <function line_dataprovider at 0x7f6a67013b90>, 'regex-line': <function regex_line_dataprovider at 0x7f6a67013cf8>}¶
-
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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ Sets the metadata information for datasets previously determined to be in bed format.
-
as_ucsc_display_file
(dataset, **kwd)[source]¶ Returns file contents with only the bed data. If bed 6+, treat as interval.
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ 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)[source]¶ 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¶
-
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)[source]¶ 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)[source]¶ 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)[source]¶ 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
-
get_estimated_display_viewport
(dataset)[source]¶ 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…
-
sniff_prefix
(file_prefix)[source]¶ 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
-
dataproviders
= {'base': <function base_dataprovider at 0x7f6a67013320>, 'chunk': <function chunk_dataprovider at 0x7f6a67013488>, 'chunk64': <function chunk64_dataprovider at 0x7f6a670135f0>, 'column': <function column_dataprovider at 0x7f6a832ce1b8>, 'dataset-column': <function dataset_column_dataprovider at 0x7f6a832ce320>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7f6a832ce5f0>, 'dict': <function dict_dataprovider at 0x7f6a832ce488>, 'genomic-region': <function genomic_region_dataprovider at 0x7f6a8409dc08>, 'genomic-region-dict': <function genomic_region_dict_dataprovider at 0x7f6a8409dd70>, 'interval': <function interval_dataprovider at 0x7f6a8409ded8>, 'interval-dict': <function interval_dict_dataprovider at 0x7f6a670680c8>, 'line': <function line_dataprovider at 0x7f6a67013b90>, 'regex-line': <function regex_line_dataprovider at 0x7f6a67013cf8>}¶
-
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)[source]¶ 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
-
sniff_prefix
(file_prefix)[source]¶ Determines whether the file is in GFF version 3 format
GFF 3 format:
- adds a mechanism for representing more than one level of hierarchical grouping of features and subfeatures.
- separates the ideas of group membership and feature name/id
- constrains the feature type field to be taken from a controlled vocabulary.
- allows a single feature, such as an exon, to belong to more than one group at a time.
- provides an explicit convention for pairwise alignments
- 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)[source]¶ 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)[source]¶ 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)[source]¶ 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'}¶
-
get_estimated_display_viewport
(dataset)[source]¶ Return a chrom, start, stop tuple for viewing a file.
-
sniff_prefix
(file_prefix)[source]¶ 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
-
dataproviders
= {'base': <function base_dataprovider at 0x7f6a67013320>, 'chunk': <function chunk_dataprovider at 0x7f6a67013488>, 'chunk64': <function chunk64_dataprovider at 0x7f6a670135f0>, 'column': <function column_dataprovider at 0x7f6a832ce1b8>, 'dataset-column': <function dataset_column_dataprovider at 0x7f6a832ce320>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7f6a832ce5f0>, 'dict': <function dict_dataprovider at 0x7f6a832ce488>, 'line': <function line_dataprovider at 0x7f6a67013b90>, 'regex-line': <function regex_line_dataprovider at 0x7f6a67013cf8>, 'wiggle': <function wiggle_dataprovider at 0x7f6a67068d70>, 'wiggle-dict': <function wiggle_dict_dataprovider at 0x7f6a67068ed8>}¶
-
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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
UCSC CustomTrack
-
edam_format
= 'format_3588'¶
-
file_ext
= 'customtrack'¶
-
get_estimated_display_viewport
(dataset, chrom_col=None, start_col=None, end_col=None)[source]¶ Return a chrom, start, stop tuple for viewing a file.
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ 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
-
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)[source]¶ 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'¶
-
-
class
galaxy.datatypes.interval.
ScIdx
(**kwd)[source]¶ 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'¶
-
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)[source]¶ 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.
-
class
galaxy.datatypes.metadata.
MetadataCollection
(parent)[source]¶ 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.
-
parent
¶
-
spec
¶
-
-
class
galaxy.datatypes.metadata.
MetadataSpecCollection
(dict=None)[source]¶ 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”.
-
class
galaxy.datatypes.metadata.
MetadataParameter
(spec)[source]¶ Bases:
object
-
classmethod
marshal
(value)[source]¶ This method should/can be overridden to convert the incoming value to whatever type it is supposed to be.
-
classmethod
-
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)[source]¶ Bases:
object
Defines a metadata element and adds it to the metadata_spec (which is a MetadataSpecCollection) of datatype.
-
class
galaxy.datatypes.metadata.
FileParameter
(spec)[source]¶ Bases:
galaxy.model.metadata.MetadataParameter
-
from_external_value
(value, parent, path_rewriter=None)[source]¶ Turns a value read from a external dict into its value to be pushed directly into the metadata dict.
-
-
class
galaxy.datatypes.metadata.
MetadataTempFile
(**kwds)[source]¶ Bases:
object
-
tmp_dir
= 'database/tmp'¶
-
file_name
¶
-
-
class
galaxy.datatypes.metadata.
JobExternalOutputMetadataWrapper
(job)[source]¶ 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)
galaxy.datatypes.molecules module¶
-
galaxy.datatypes.molecules.
count_special_lines
(word, filename, invert=False)[source]¶ 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)[source]¶ counting the number of lines from the ‘filename’ file
-
class
galaxy.datatypes.molecules.
GenericMolFile
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
Abstract class for most of the molecule files.
-
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)[source]¶ Bases:
galaxy.datatypes.molecules.GenericMolFile
-
file_ext
= 'mol'¶
-
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)[source]¶ Bases:
galaxy.datatypes.molecules.GenericMolFile
-
file_ext
= 'sdf'¶
-
sniff_prefix
(file_prefix)[source]¶ 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
-
classmethod
split
(input_datasets, subdir_generator_function, split_params)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.molecules.GenericMolFile
-
file_ext
= 'mol2'¶
-
sniff_prefix
(file_prefix)[source]¶ 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
-
classmethod
split
(input_datasets, subdir_generator_function, split_params)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.molecules.GenericMolFile
chemfp fingerprint file: http://code.google.com/p/chem-fingerprints/wiki/FPS
-
file_ext
= 'fps'¶
-
sniff_prefix
(file_prefix)[source]¶ 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
-
classmethod
split
(input_datasets, subdir_generator_function, split_params)[source]¶ Split the input files by fingerprint records.
-
static
merge
(split_files, output_file)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.binary.Binary
OpenBabel Fastsearch format (fs).
-
file_ext
= 'obfs'¶
-
composite_type
= 'basic'¶
-
allow_datatype_change
= False¶
-
__init__
(**kwd)[source]¶ A Fastsearch Index consists of a binary file with the fingerprints and a pointer the actual molecule file.
-
display_data
(trans, data, preview=False, filename=None, to_ext=None, **kwd)[source]¶ Apparently an old display method, but still gets called.
This allows us to format the data shown in the central pane via the “eye” icon.
-
merge
(split_files, output_file, extra_merge_args)[source]¶ Merging Fastsearch indices is not supported.
-
split
(input_datasets, subdir_generator_function, split_params)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.molecules.GenericMolFile
-
file_ext
= 'drf'¶
-
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)[source]¶ Bases:
galaxy.datatypes.molecules.GenericMolFile
Pharmacophore database format from silicos-it.
-
file_ext
= 'phar'¶
-
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)[source]¶ Bases:
galaxy.datatypes.molecules.GenericMolFile
Protein Databank format. http://www.wwpdb.org/documentation/format33/v3.3.html
-
file_ext
= 'pdb'¶
-
sniff_prefix
(file_prefix)[source]¶ 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
-
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)[source]¶ 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)[source]¶ 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
-
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)[source]¶ Bases:
galaxy.datatypes.data.Text
-
file_ext
= 'grd'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
-
class
galaxy.datatypes.molecules.
grdtgz
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
-
file_ext
= 'grd.tgz'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.molecules.
InChI
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'inchi'¶
-
column_names
= ['InChI']¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'smi'¶
-
column_names
= ['SMILES', 'TITLE']¶
-
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)[source]¶ Bases:
galaxy.datatypes.xml.GenericXml
Chemical Markup Language http://cml.sourceforge.net/
-
file_ext
= 'cml'¶
-
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)¶
-
sniff_prefix
(file_prefix)[source]¶ 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
-
galaxy.datatypes.mothur module¶
Mothur Metagenomics Datatypes
-
class
galaxy.datatypes.mothur.
Otu
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
-
file_ext
= 'mothur.otu'¶
-
set_meta
(dataset, overwrite=True, **kwd)[source]¶ 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)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.mothur.Otu
-
file_ext
= 'mothur.sabund'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.mothur.Otu
-
file_ext
= 'mothur.shared'¶
-
sniff_prefix
(file_prefix, vals_are_int=False)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.map'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.align.check'¶
-
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)[source]¶ 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'¶
-
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)[source]¶ Bases:
galaxy.datatypes.data.Text
-
file_ext
= 'mothur.dist'¶ Add metadata elements
-
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)[source]¶ Bases:
galaxy.datatypes.mothur.DistanceMatrix
-
file_ext
= 'mothur.lower.dist'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.mothur.DistanceMatrix
-
file_ext
= 'mothur.square.dist'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.mothur.DistanceMatrix
,galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.pair.dist'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.names'¶
-
__init__
(**kwd)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.summary'¶
-
__init__
(**kwd)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.groups'¶
-
__init__
(**kwd)[source]¶ http://www.mothur.org/wiki/Groups_file Group file assigns sequence (col 1) to a group (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 ' ', groups (MetadataParameter): Group Names, defaults to '[]'¶
-
-
class
galaxy.datatypes.mothur.
AccNos
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.accnos'¶
-
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)[source]¶ Bases:
galaxy.datatypes.data.Text
-
file_ext
= 'mothur.oligos'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.freq'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.quan'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.data.Text
-
file_ext
= 'mothur.filter'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.count_table'¶
-
__init__
(**kwd)[source]¶ 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
-
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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.ref.taxonomy'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.cons.taxonomy'¶
-
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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.tax.summary'¶
-
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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.axes'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ 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 …
-
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'¶
-
galaxy.datatypes.msa module¶
-
class
galaxy.datatypes.msa.
InfernalCM
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
-
file_ext
= 'cm'¶
-
sniff_prefix
(file_prefix)[source]¶ >>> 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
-
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)[source]¶ Bases:
galaxy.datatypes.data.Text
-
edam_data
= 'data_1364'¶
-
edam_format
= 'format_1370'¶
-
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)[source]¶ Bases:
galaxy.datatypes.msa.Hmmer
-
edam_format
= 'format_3328'¶
-
file_ext
= 'hmm2'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
-
class
galaxy.datatypes.msa.
Hmmer3
(**kwd)[source]¶ Bases:
galaxy.datatypes.msa.Hmmer
-
edam_format
= 'format_3329'¶
-
file_ext
= 'hmm3'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
-
class
galaxy.datatypes.msa.
HmmerPress
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class for hmmpress database files.
-
file_ext
= 'hmmpress'¶
-
allow_datatype_change
= False¶
-
composite_type
= 'basic'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.msa.
Stockholm_1_0
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
-
edam_data
= 'data_0863'¶
-
edam_format
= 'format_1961'¶
-
file_ext
= 'stockholm'¶
-
classmethod
split
(input_datasets, subdir_generator_function, split_params)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.data.Text
-
file_ext
= 'xmfa'¶
-
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'¶
-
sniff
(filename)¶
-
galaxy.datatypes.neo4j module¶
Neo4j Composite Dataset
-
class
galaxy.datatypes.neo4j.
Neo4j
(**kwd)[source]¶ 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)[source]¶ This is called only at upload to write the html file cannot rename the datasets here - they come with the default unfortunately
-
display_data
(trans, data, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd)[source]¶ Documented as an old display method, but still gets called via tests etc This allows us to format the data shown in the central pane via the “eye” icon.
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
-
class
galaxy.datatypes.neo4j.
Neo4jDB
(**kwd)[source]¶ 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¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
-
class
galaxy.datatypes.neo4j.
Neo4jDBzip
(**kwd)[source]¶ 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¶
-
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)[source]¶ 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)[source]¶ This is called only at upload to write the html file cannot rename the datasets here - they come with the default unfortunately
-
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)[source]¶ 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)[source]¶ 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.proteomics module¶
Proteomics Datatypes
-
class
galaxy.datatypes.proteomics.
Wiff
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.proteomics.
PepXmlReport
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
pepxml converted to tabular report
-
edam_data
= 'data_2536'¶
-
file_ext
= 'pepxml.tsv'¶
-
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)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
protxml converted to tabular report
-
edam_data
= 'data_2536'¶
-
file_ext
= 'protxml.tsv'¶
-
comment_lines
= 1¶
-
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)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
-
class
galaxy.datatypes.proteomics.
PepXml
(**kwd)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.data.Text
Mascot Generic Format data
-
edam_data
= 'data_2536'¶
-
edam_format
= 'format_3651'¶
-
file_ext
= 'mgf'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
-
class
galaxy.datatypes.proteomics.
MascotDat
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
Mascot search results
-
edam_data
= 'data_2536'¶
-
edam_format
= 'format_3713'¶
-
file_ext
= 'mascotdat'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
-
class
galaxy.datatypes.proteomics.
ThermoRAW
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class describing a Thermo Finnigan binary RAW file
-
edam_data
= 'data_2536'¶
-
edam_format
= 'format_3712'¶
-
file_ext
= 'raw'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.proteomics.
Msp
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
Output of NIST MS Search Program chemdata.nist.gov/mass-spc/ftp/mass-spc/PepLib.pdf
-
file_ext
= 'msp'¶
-
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)[source]¶ Bases:
galaxy.datatypes.data.Text
SPlib without index file
-
file_ext
= 'splib_noindex'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
-
class
galaxy.datatypes.proteomics.
SPLib
(**kwd)[source]¶ Bases:
galaxy.datatypes.proteomics.Msp
SpectraST Spectral Library. Closely related to msp format
-
file_ext
= 'splib'¶
-
composite_type
= 'auto_primary_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)[source]¶ Bases:
galaxy.datatypes.data.Text
-
file_ext
= 'ms2'¶
-
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)[source]¶ 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)[source]¶ 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)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
-
class
galaxy.datatypes.proteomics.
Analyze75
(**kwd)[source]¶ 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'¶
-
metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
-
galaxy.datatypes.qualityscore module¶
Qualityscore class
-
class
galaxy.datatypes.qualityscore.
QualityScore
(**kwd)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.qualityscore.QualityScore
until we know more about quality score formats
-
edam_format
= 'format_3610'¶
-
file_ext
= 'qualsolid'¶
-
sniff_prefix
(file_prefix)[source]¶ >>> 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
-
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)[source]¶ Bases:
galaxy.datatypes.qualityscore.QualityScore
until we know more about quality score formats
-
edam_format
= 'format_3611'¶
-
file_ext
= 'qual454'¶
-
sniff_prefix
(file_prefix)[source]¶ >>> 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)[source]¶ 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)[source]¶ 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
[source]¶ Bases:
exceptions.Exception
-
class
galaxy.datatypes.registry.
Registry
(config=None)[source]¶ Bases:
object
-
load_datatypes
(root_dir=None, config=None, deactivate=False, override=True)[source]¶ 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.
-
load_datatype_sniffers
(root, deactivate=False, handling_proprietary_datatypes=False, override=False, compressed_sniffers=None)[source]¶ 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.
-
get_datatype_class_by_name
(name)[source]¶ Return the datatype class where the datatype’s type attribute (as defined in the datatype_conf.xml file) contains name.
-
get_mimetype_by_extension
(ext, default='application/octet-stream')[source]¶ Returns a mimetype based on an extension
-
load_datatype_converters
(toolbox, installed_repository_dict=None, deactivate=False, use_cached=False)[source]¶ 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)[source]¶ 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)[source]¶ Reloads display applications: by id, or all if no ids provided Returns tuple( [reloaded_ids], [failed_ids] )
-
get_converter_by_target_type
(source_ext, target_ext)[source]¶ Returns a converter based on source and target datatypes
-
find_conversion_destination_for_dataset_by_extensions
(dataset_or_ext, accepted_formats, converter_safe=True)[source]¶ Returns ( target_ext, existing converted dataset )
-
get_upload_metadata_params
(context, group, tool)[source]¶ Returns dict of case value:inputs for metadata conditional for upload tool
-
edam_formats
¶
-
edam_data
¶
-
galaxy.datatypes.sequence module¶
Sequence classes
-
class
galaxy.datatypes.sequence.
SequenceSplitLocations
(**kwd)[source]¶ 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'¶
-
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)[source]¶ Bases:
galaxy.datatypes.data.Text
Class describing a sequence
-
edam_data
= 'data_2044'¶ Add metadata elements
-
set_meta
(dataset, **kwd)[source]¶ Set the number of sequences and the number of data lines in dataset.
-
classmethod
do_fast_split
(input_datasets, toc_file_datasets, subdir_generator_function, split_params)[source]¶
-
classmethod
write_split_files
(input_datasets, toc_file_datasets, subdir_generator_function, sequences_per_file)[source]¶
-
split
(input_datasets, subdir_generator_function, split_params)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.data.Text
Class describing an alignment
-
edam_data
= 'data_0863'¶ Add metadata elements
-
split
(input_datasets, subdir_generator_function, split_params)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.sequence.Sequence
Class representing a FASTA sequence
-
edam_format
= 'format_1929'¶
-
file_ext
= 'fasta'¶
-
sniff_prefix
(file_prefix)[source]¶ 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)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.sequence.Sequence
Class representing the SOLID Color-Space sequence ( csfasta )
-
edam_format
= 'format_3589'¶
-
file_ext
= 'csfasta'¶
-
sniff_prefix
(file_prefix)[source]¶ - 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
-
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)[source]¶ Bases:
galaxy.datatypes.sequence.Sequence
Base class for FastQ sequences
-
edam_format
= 'format_1930'¶
-
file_ext
= 'fastq'¶
-
set_meta
(dataset, **kwd)[source]¶ 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)[source]¶ 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
-
classmethod
split
(input_datasets, subdir_generator_function, split_params)[source]¶ FASTQ files are split on cluster boundaries, in increments of 4 lines
-
static
process_split_file
(data)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ Bases:
galaxy.datatypes.sequence.Alignment
Class describing a Maf alignment
-
edam_format
= 'format_3008'¶
-
file_ext
= 'maf'¶
-
set_meta
(dataset, overwrite=True, **kwd)[source]¶ Parses and sets species, chromosomes, index from MAF file.
-
sniff_prefix
(file_prefix)[source]¶ 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
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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'¶
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sniff
(filename)¶
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class
galaxy.datatypes.sequence.
MafCustomTrack
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
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file_ext
= 'mafcustomtrack'¶
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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'¶
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class
galaxy.datatypes.sequence.
Axt
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
Class describing an axt alignment
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edam_data
= 'data_0863'¶
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edam_format
= 'format_3013'¶
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file_ext
= 'axt'¶
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sniff_prefix
(file_prefix)[source]¶ 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
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metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
sniff
(filename)¶
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class
galaxy.datatypes.sequence.
Lav
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
Class describing a LAV alignment
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edam_data
= 'data_0863'¶
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edam_format
= 'format_3014'¶
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file_ext
= 'lav'¶
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sniff_prefix
(file_prefix)[source]¶ 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
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metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
-
sniff
(filename)¶
-
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class
galaxy.datatypes.sequence.
RNADotPlotMatrix
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Data
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edam_format
= 'format_3466'¶
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file_ext
= 'rna_eps'¶
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metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?'¶
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class
galaxy.datatypes.sequence.
DotBracket
(**kwd)[source]¶ Bases:
galaxy.datatypes.sequence.Sequence
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edam_data
= 'data_0880'¶
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edam_format
= 'format_1457'¶
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file_ext
= 'dbn'¶
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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'¶
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sniff
(filename)¶
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sequence_regexp
= <_sre.SRE_Pattern object>¶
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structure_regexp
= <_sre.SRE_Pattern object>¶
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set_meta
(dataset, **kwd)[source]¶ Set the number of sequences and the number of data lines in dataset.
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sniff_prefix
(file_prefix)[source]¶ 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.
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class
galaxy.datatypes.sequence.
Genbank
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
Class representing a Genbank sequence
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metadata_spec
= dbkey (DBKeyParameter): Database/Build, defaults to '?', data_lines (MetadataParameter): Number of data lines, defaults to '0'¶
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sniff
(filename)¶
-
edam_format
= 'format_1936'¶
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edam_data
= 'data_0849'¶
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file_ext
= 'genbank'¶
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