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galaxy.datatypes package¶
Subpackages¶
- galaxy.datatypes.converters package
- Submodules
- galaxy.datatypes.converters.bed_to_gff_converter module
- galaxy.datatypes.converters.bedgraph_to_array_tree_converter module
- galaxy.datatypes.converters.bgzip module
- galaxy.datatypes.converters.cram_to_bam module
- galaxy.datatypes.converters.fasta_to_len module
- galaxy.datatypes.converters.fasta_to_tabular_converter module
- galaxy.datatypes.converters.fastq_to_fqtoc module
- galaxy.datatypes.converters.fastqsolexa_to_fasta_converter module
- galaxy.datatypes.converters.fastqsolexa_to_qual_converter module
- galaxy.datatypes.converters.gff_to_bed_converter module
- galaxy.datatypes.converters.gff_to_interval_index_converter module
- galaxy.datatypes.converters.interval_to_bed_converter module
- galaxy.datatypes.converters.interval_to_bedstrict_converter module
- galaxy.datatypes.converters.interval_to_coverage module
- galaxy.datatypes.converters.interval_to_fli module
- galaxy.datatypes.converters.interval_to_interval_index_converter module
- galaxy.datatypes.converters.interval_to_tabix_converter module
- galaxy.datatypes.converters.lped_to_fped_converter module
- galaxy.datatypes.converters.lped_to_pbed_converter module
- galaxy.datatypes.converters.maf_to_fasta_converter module
- galaxy.datatypes.converters.maf_to_interval_converter module
- galaxy.datatypes.converters.pbed_ldreduced_converter module
- galaxy.datatypes.converters.pbed_to_lped_converter module
- galaxy.datatypes.converters.picard_interval_list_to_bed6_converter module
- galaxy.datatypes.converters.pileup_to_interval_index_converter module
- galaxy.datatypes.converters.ref_to_seq_taxonomy_converter module
- galaxy.datatypes.converters.sam_to_bam module
- galaxy.datatypes.converters.tabular_csv 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.annotation module¶
-
class
galaxy.datatypes.annotation.
SnapHmm
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
-
file_ext
= 'snaphmm'¶
-
edam_data
= 'data_1364'¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4803804e90>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
sniff
(filename)¶
-
-
class
galaxy.datatypes.annotation.
Augustus
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.CompressedArchive
Class describing an Augustus prediction model
-
file_ext
= 'augustus'¶
-
edam_data
= 'data_0950'¶
-
compressed
= True¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805722050>}¶
-
galaxy.datatypes.anvio module¶
Datatypes for Anvi’o https://github.com/merenlab/anvio
-
class
galaxy.datatypes.anvio.
AnvioComposite
(**kwd)[source]¶ Bases:
galaxy.datatypes.text.Html
Base class to use for Anvi’o composite datatypes. Generally consist of a sqlite database, plus optional additional files
-
file_ext
= 'anvio_composite'¶
-
composite_type
= 'auto_primary_file'¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bb0a90>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.anvio.
AnvioDB
(*args, **kwd)[source]¶ Bases:
galaxy.datatypes.anvio.AnvioComposite
Class for AnvioDB database files.
-
file_ext
= 'anvio_db'¶
-
composite_type
= 'auto_primary_file'¶
-
allow_datatype_change
= False¶
-
set_meta
(dataset, **kwd)[source]¶ Set the anvio_basename based upon actual extra_files_path contents.
-
metadata_spec
= {'anvio_basename': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bb0c50>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bb0a90>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.anvio.
AnvioStructureDB
(*args, **kwd)[source]¶ Bases:
galaxy.datatypes.anvio.AnvioDB
Class for Anvio Structure DB database files.
-
file_ext
= 'anvio_structure_db'¶
-
composite_type
= 'auto_primary_file'¶
-
allow_datatype_change
= False¶
-
metadata_spec
= {'anvio_basename': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bb0e90>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bb0a90>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.anvio.
AnvioGenomesDB
(*args, **kwd)[source]¶ Bases:
galaxy.datatypes.anvio.AnvioDB
Class for Anvio Genomes DB database files.
-
file_ext
= 'anvio_genomes_db'¶
-
composite_type
= 'auto_primary_file'¶
-
allow_datatype_change
= False¶
-
metadata_spec
= {'anvio_basename': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bba0d0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bb0a90>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.anvio.
AnvioContigsDB
(*args, **kwd)[source]¶ Bases:
galaxy.datatypes.anvio.AnvioDB
Class for Anvio Contigs DB database files.
-
file_ext
= 'anvio_contigs_db'¶
-
composite_type
= 'auto_primary_file'¶
-
allow_datatype_change
= False¶
-
metadata_spec
= {'anvio_basename': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bba310>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bb0a90>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.anvio.
AnvioProfileDB
(*args, **kwd)[source]¶ Bases:
galaxy.datatypes.anvio.AnvioDB
Class for Anvio Profile DB database files.
-
file_ext
= 'anvio_profile_db'¶
-
composite_type
= 'auto_primary_file'¶
-
allow_datatype_change
= False¶
-
metadata_spec
= {'anvio_basename': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bba4d0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bb0a90>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.anvio.
AnvioPanDB
(*args, **kwd)[source]¶ Bases:
galaxy.datatypes.anvio.AnvioDB
Class for Anvio Pan DB database files.
-
file_ext
= 'anvio_pan_db'¶
-
composite_type
= 'auto_primary_file'¶
-
allow_datatype_change
= False¶
-
metadata_spec
= {'anvio_basename': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bba710>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bb0a90>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.anvio.
AnvioSamplesDB
(*args, **kwd)[source]¶ Bases:
galaxy.datatypes.anvio.AnvioDB
Class for Anvio Samples DB database files.
-
file_ext
= 'anvio_samples_db'¶
-
composite_type
= 'auto_primary_file'¶
-
allow_datatype_change
= False¶
-
metadata_spec
= {'anvio_basename': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bba950>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802bb0a90>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4803db09d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'sequences': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805938210>}¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4803f6b5d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4803f6bed0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'long_reads': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4803f6bad0>, 'paired_end_reads': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4803f6b2d0>, 'short2_reads': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4803f6b150>}¶
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1990>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1c10>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1e50>}¶
-
-
class
galaxy.datatypes.binary.
Cel
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Cel File format described at: http://media.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html
-
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(‘affy_v_agcc.cel’) >>> Cel().sniff(fname) True >>> fname = get_test_fname(‘affy_v_3.cel’) >>> Cel().sniff(fname) True >>> fname = get_test_fname(‘affy_v_4.cel’) >>> Cel().sniff(fname) True >>> fname = get_test_fname(‘test.gal’) >>> Cel().sniff(fname) False
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1990>, 'version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e6110>}¶
-
-
class
galaxy.datatypes.binary.
MashSketch
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Mash Sketch file. Sketches are used by the MinHash algorithm to allow fast distance estimations with low storage and memory requirements. To make a sketch, each k-mer in a sequence is hashed, which creates a pseudo-random identifier. By sorting these identifiers (hashes), a small subset from the top of the sorted list can represent the entire sequence (these are min-hashes). The more similar another sequence is, the more min-hashes it is likely to share.
-
file_ext
= 'msh'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e6350>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e65d0>}¶
-
-
class
galaxy.datatypes.binary.
DynamicCompressedArchive
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.CompressedArchive
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e6810>}¶
-
-
class
galaxy.datatypes.binary.
GzDynamicCompressedArchive
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.DynamicCompressedArchive
-
compressed_format
= 'gzip'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e6a50>}¶
-
-
class
galaxy.datatypes.binary.
Bz2DynamicCompressedArchive
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.DynamicCompressedArchive
-
compressed_format
= 'bz2'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e6c90>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e6f10>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6190>}¶
-
-
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
= {'bam_header': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6750>, 'bam_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f64d0>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f68d0>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6850>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f67d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e65d0>, 'read_groups': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f65d0>, 'reference_lengths': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f66d0>, 'reference_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6650>, 'sort_order': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6550>}¶
-
-
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 0x7f482d4d28c0>, 'chunk': <function chunk_dataprovider at 0x7f482d4d2a28>, 'chunk64': <function chunk64_dataprovider at 0x7f482d4d2b90>, 'column': <function column_dataprovider at 0x7f482a5f1f50>, 'dict': <function dict_dataprovider at 0x7f482a5f7140>, 'genomic-region': <function genomic_region_dataprovider at 0x7f482a5f7578>, 'genomic-region-dict': <function genomic_region_dict_dataprovider at 0x7f482a5f76e0>, 'header': <function header_dataprovider at 0x7f482a5f72a8>, 'id-seq-qual': <function id_seq_qual_dataprovider at 0x7f482a5f7410>, 'line': <function line_dataprovider at 0x7f482a5f1c80>, 'regex-line': <function regex_line_dataprovider at 0x7f482a5f1de8>, 'samtools': <function samtools_dataprovider at 0x7f482a5f7848>}¶
-
metadata_spec
= {'bam_header': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6750>, 'bam_index': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6fd0>, 'bam_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f64d0>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f68d0>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6850>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f67d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e65d0>, 'read_groups': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f65d0>, 'reference_lengths': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f66d0>, 'reference_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6650>, 'sort_order': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6550>}¶
-
-
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
= {'bam_header': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6750>, 'bam_index': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8250>, 'bam_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f64d0>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f68d0>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6850>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f67d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e65d0>, 'read_groups': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f65d0>, 'reference_lengths': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f66d0>, 'reference_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6650>, 'sort_order': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f6550>}¶
-
-
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
= {'bam_header': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8710>, 'bam_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8490>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8890>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8810>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8790>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e65d0>, 'read_groups': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8590>, 'reference_lengths': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8690>, 'reference_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8610>, 'sort_order': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8510>}¶
-
-
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
= {'bam_header': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8d50>, 'bam_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8ad0>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8ed0>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8e50>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8dd0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e65d0>, 'read_groups': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8bd0>, 'reference_lengths': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8cd0>, 'reference_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8c50>, 'sort_order': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5f8b50>}¶
-
-
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
= {'cram_index': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5fc250>, 'cram_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5fc1d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1990>}¶
-
-
class
galaxy.datatypes.binary.
BaseBcf
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.CompressedArchive
-
edam_format
= 'format_3020'¶
-
edam_data
= 'data_3498'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5fc490>}¶
-
-
class
galaxy.datatypes.binary.
Bcf
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.BaseBcf
Class describing a (BGZF-compressed) BCF file
-
file_ext
= 'bcf'¶
-
metadata_spec
= {'bcf_index': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5fc750>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5fc490>}¶
-
-
class
galaxy.datatypes.binary.
BcfUncompressed
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.BaseBcf
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5fc990>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5fcc10>}¶
-
-
class
galaxy.datatypes.binary.
Loom
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.H5
Class describing a Loom file: http://loompy.org/
>>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname('test.loom') >>> Loom().sniff(fname) True >>> fname = get_test_fname('test.mz5') >>> Loom().sniff(fname) False
-
file_ext
= 'loom'¶
-
edam_format
= 'format_3590'¶
-
metadata_spec
= {'col_attrs_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601490>, 'col_attrs_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601510>, 'col_graphs_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601590>, 'col_graphs_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601610>, 'creation_date': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601190>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5fcc10>, 'description': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5fcf50>, 'doi': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601090>, 'layers_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601290>, 'layers_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601310>, 'loom_spec_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601110>, 'row_attrs_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601390>, 'row_attrs_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601410>, 'row_graphs_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601690>, 'row_graphs_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601710>, 'shape': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601210>, 'title': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5fced0>, 'url': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5fcfd0>}¶
-
-
class
galaxy.datatypes.binary.
Anndata
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.H5
Class describing an HDF5 anndata files: http://anndata.rtfd.io >>> from galaxy.datatypes.sniff import get_test_fname >>> Anndata().sniff(get_test_fname(‘pbmc3k_tiny.h5ad’)) True >>> Anndata().sniff(get_test_fname(‘test.mz5’)) False
-
file_ext
= 'h5ad'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601950>}¶
-
-
class
galaxy.datatypes.binary.
GmxBinary
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Base class for GROMACS binary files - xtc, trr, cpt
-
magic_number
= None¶
-
file_ext
= ''¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601c10>}¶
-
-
class
galaxy.datatypes.binary.
Trr
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.GmxBinary
Class describing an trr file from the GROMACS suite
>>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname('md.trr') >>> Trr().sniff(fname) True >>> fname = get_test_fname('interval.interval') >>> Trr().sniff(fname) False
-
file_ext
= 'trr'¶
-
magic_number
= 1993¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a601e50>}¶
-
-
class
galaxy.datatypes.binary.
Cpt
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.GmxBinary
Class describing a checkpoint (.cpt) file from the GROMACS suite
>>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname('md.cpt') >>> Cpt().sniff(fname) True >>> fname = get_test_fname('md.trr') >>> Cpt().sniff(fname) False
-
file_ext
= 'cpt'¶
-
magic_number
= 171817¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a6040d0>}¶
-
-
class
galaxy.datatypes.binary.
Xtc
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.GmxBinary
Class describing an xtc file from the GROMACS suite
>>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname('md.xtc') >>> Xtc().sniff(fname) True >>> fname = get_test_fname('md.trr') >>> Xtc().sniff(fname) False
-
file_ext
= 'xtc'¶
-
magic_number
= 1995¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a604310>}¶
-
-
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.biom2') >>> 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
= {'creation_date': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a6048d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5fcc10>, 'format': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a604750>, 'format_url': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a604650>, 'format_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a6046d0>, 'generated_by': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a604850>, 'id': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a6045d0>, 'nnz': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a604950>, 'shape': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a6049d0>, 'type': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a6047d0>}¶
-
-
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.biom2') >>> Cool().sniff(fname) False
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a604c50>}¶
-
-
class
galaxy.datatypes.binary.
MCool
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.H5
Class describing the multi-resolution cool format (https://github.com/mirnylab/cooler)
-
file_ext
= 'mcool'¶
-
sniff
(filename)[source]¶ >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname('matrix.mcool') >>> MCool().sniff(fname) True >>> fname = get_test_fname('matrix.cool') >>> MCool().sniff(fname) False >>> fname = get_test_fname('test.mz5') >>> MCool().sniff(fname) False >>> fname = get_test_fname('wiggle.wig') >>> MCool().sniff(fname) False >>> fname = get_test_fname('biom2_sparse_otu_table_hdf5.biom2') >>> MCool().sniff(fname) False
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a604ed0>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58a190>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58a410>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58a690>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58a8d0>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58ab50>}¶
-
-
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 0x7f482d4d28c0>, 'chunk': <function chunk_dataprovider at 0x7f482d4d2a28>, 'chunk64': <function chunk64_dataprovider at 0x7f482d4d2b90>, 'sqlite': <function sqlite_dataprovider at 0x7f482a58d500>, 'sqlite-dict': <function sqlite_datadictprovider at 0x7f482a58d7d0>, 'sqlite-table': <function sqlite_datatableprovider at 0x7f482a58d668>}¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1990>, 'table_columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f090>, 'table_row_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f110>, 'tables': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58afd0>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1990>, 'gemini_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f3d0>, 'table_columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f090>, 'table_row_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f110>, 'tables': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58afd0>}¶
-
-
class
galaxy.datatypes.binary.
CuffDiffSQlite
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.SQlite
Class describing a CuffDiff SQLite database
-
file_ext
= 'cuffdiff.sqlite'¶
-
edam_format
= 'format_3621'¶
-
metadata_spec
= {'cuffdiff_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f690>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1990>, 'genes': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f710>, 'samples': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f790>, 'table_columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f090>, 'table_row_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f110>, 'tables': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58afd0>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1990>, 'table_columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58fa90>, 'table_row_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58fb10>, 'tables': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58fa10>}¶
-
-
class
galaxy.datatypes.binary.
BlibSQlite
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.SQlite
Class describing a Proteomics Spectral Library Sqlite database
-
file_ext
= 'blib'¶
-
metadata_spec
= {'blib_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58fdd0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1990>, 'table_columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f090>, 'table_row_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f110>, 'tables': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58afd0>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1990>, 'table_columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a594150>, 'table_row_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5941d0>, 'tables': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5940d0>}¶
-
-
class
galaxy.datatypes.binary.
GAFASQLite
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.SQlite
Class describing a GAFA SQLite database
-
file_ext
= 'gafa.sqlite'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1990>, 'gafa_schema_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a594450>, 'table_columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f090>, 'table_row_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58f110>, 'tables': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a58afd0>}¶
-
-
class
galaxy.datatypes.binary.
Xlsx
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class for Excel 2007 (xlsx) files
-
file_ext
= 'xlsx'¶
-
compressed
= True¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a594690>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a594910>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a594b90>}¶
-
-
class
galaxy.datatypes.binary.
RData
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Generic R Data file datatype implementation
-
file_ext
= 'rdata'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a594dd0>}¶
-
-
class
galaxy.datatypes.binary.
OxliBinary
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a599050>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a599290>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5994d0>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a599710>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a599950>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a599b90>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a599dd0>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e65d0>, 'version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5a40d0>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e65d0>, 'fast5_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5a4390>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e65d0>, 'fast5_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5a45d0>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e65d0>, 'fast5_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5a4810>}¶
-
-
class
galaxy.datatypes.binary.
SearchGuiArchive
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.CompressedArchive
Class describing a SearchGUI archive
-
file_ext
= 'searchgui_archive'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e65d0>, 'searchgui_major_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5a4b50>, 'searchgui_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5a4ad0>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5a4dd0>}¶
-
-
class
galaxy.datatypes.binary.
Dcd
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class describing a dcd file from the CHARMM molecular simulation program
>>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname('test_glucose_vacuum.dcd') >>> Dcd().sniff(fname) True >>> fname = get_test_fname('interval.interval') >>> Dcd().sniff(fname) False
-
file_ext
= 'dcd'¶
-
edam_data
= 'data_3842'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5ae090>}¶
-
-
class
galaxy.datatypes.binary.
Vel
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class describing a velocity file from the CHARMM molecular simulation program
>>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname('test_charmm.vel') >>> Vel().sniff(fname) True >>> fname = get_test_fname('interval.interval') >>> Vel().sniff(fname) False
-
file_ext
= 'vel'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5ae310>}¶
-
-
class
galaxy.datatypes.binary.
DAA
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class describing an DAA (diamond alignment archive) file >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname(‘diamond.daa’) >>> DAA().sniff(fname) True >>> fname = get_test_fname(‘interval.interval’) >>> DAA().sniff(fname) False
-
file_ext
= 'daa'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5ae550>}¶
-
-
class
galaxy.datatypes.binary.
RMA6
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class describing an RMA6 (MEGAN6 read-match archive) file >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname(‘diamond.rma6’) >>> RMA6().sniff(fname) True >>> fname = get_test_fname(‘interval.interval’) >>> RMA6().sniff(fname) False
-
file_ext
= 'rma6'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5ae790>}¶
-
-
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'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5ae9d0>}¶
-
-
class
galaxy.datatypes.binary.
ICM
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class describing an ICM (interpolated context model) file, used by Glimmer
-
file_ext
= 'icm'¶
-
edam_data
= 'data_0950'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5aec50>}¶
-
-
class
galaxy.datatypes.binary.
BafTar
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.CompressedArchive
Base class for common behavior of tar files of directory-based raw file formats >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname(‘brukerbaf.d.tar’) >>> BafTar().sniff(fname) True >>> fname = get_test_fname(‘test.fast5.tar’) >>> BafTar().sniff(fname) False
-
edam_data
= 'data_2536'¶
-
edam_format
= 'format_3712'¶
-
file_ext
= 'brukerbaf.d.tar'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5aeed0>}¶
-
-
class
galaxy.datatypes.binary.
YepTar
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.BafTar
A tar’d up .d directory containing Agilent/Bruker YEP format data
-
file_ext
= 'agilentbrukeryep.d.tar'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5b7150>}¶
-
-
class
galaxy.datatypes.binary.
TdfTar
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.BafTar
A tar’d up .d directory containing Bruker TDF format data
-
file_ext
= 'brukertdf.d.tar'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5b73d0>}¶
-
-
class
galaxy.datatypes.binary.
MassHunterTar
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.BafTar
A tar’d up .d directory containing Agilent MassHunter format data
-
file_ext
= 'agilentmasshunter.d.tar'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5b7610>}¶
-
-
class
galaxy.datatypes.binary.
MassLynxTar
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.BafTar
A tar’d up .d directory containing Waters MassLynx format data
-
file_ext
= 'watersmasslynx.raw.tar'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5b7850>}¶
-
-
class
galaxy.datatypes.binary.
WiffTar
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.BafTar
A tar’d up .wiff/.scan pair containing Sciex WIFF format data >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname(‘some.wiff.tar’) >>> WiffTar().sniff(fname) True >>> fname = get_test_fname(‘brukerbaf.d.tar’) >>> WiffTar().sniff(fname) False >>> fname = get_test_fname(‘test.fast5.tar’) >>> WiffTar().sniff(fname) False
-
file_ext
= 'wiff.tar'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5b7a90>}¶
-
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.blastxml') >>> 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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802405e50>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48023a0090>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48023a0190>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48023a02d0>}¶
-
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
= {'chrom': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802257e90>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1150>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'length': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802257d10>}¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'face': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802257ad0>, 'file_format': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802257910>, 'other_elements': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802257850>, 'vertex': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48022571d0>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1990>, 'face': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48024c6750>, 'file_format': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802257450>, 'other_elements': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802422990>, 'vertex': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802257590>}¶
-
-
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
= {'cells': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802436b50>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dataset_type': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48022b1750>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'dimensions': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48022b1690>, 'field_components': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48023a0ad0>, 'field_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802436410>, 'file_format': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48022b12d0>, 'lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802286250>, 'origin': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4803a29f90>, 'points': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48022868d0>, 'polygons': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802286a10>, 'spacing': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802286850>, 'triangle_strips': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48024360d0>, 'vertices': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802286890>, 'vtk_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48022b1310>}¶
-
-
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
= {'cells': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802219a10>, 'dataset_type': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48023a0890>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1990>, 'dimensions': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48023a0d10>, 'field_components': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802219f50>, 'field_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48022198d0>, 'file_format': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48023a07d0>, 'lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802219650>, 'origin': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802219410>, 'points': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802219310>, 'polygons': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802219a90>, 'spacing': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48022196d0>, 'triangle_strips': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802219b90>, 'vertices': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48022193d0>, 'vtk_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48023a0f90>}¶
-
-
class
galaxy.datatypes.constructive_solid_geometry.
STL
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Data
-
file_ext
= 'stl'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48022c8910>}¶
-
galaxy.datatypes.coverage module¶
Coverage datatypes
-
class
galaxy.datatypes.coverage.
LastzCoverage
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'coverage'¶
-
metadata_spec
= {'chromCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801f519d0>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801f514d0>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'forwardCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801f51a90>, 'positionCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801f51fd0>, 'reverseCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801f51e50>}¶
-
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'>
-
edam_data
= 'data_0006'¶
-
edam_format
= 'format_1915'¶
-
file_ext
= 'data'¶
-
CHUNKABLE
= False¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶ Dictionary of metadata fields for this datatype
-
copy_safe_peek
= True¶
-
is_binary
= True¶
-
allow_datatype_change
= True¶
-
composite_type
= None¶
-
primary_file_name
= 'index'¶
-
track_type
= None¶
-
data_sources
= {}¶
-
supported_display_apps
= {}¶
-
composite_files
= {}¶
-
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.
-
groom_dataset_content
(file_name)[source]¶ This function is called on an output dataset file if dataset_content_needs_grooming returns True.
-
set_meta
(dataset, overwrite=True, **kwd)[source]¶ Unimplemented method, allows guessing of metadata from contents of file
-
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
¶
-
set_peek
(dataset, is_multi_byte=False)[source]¶ Set the peek and blurb text
Parameters: is_multi_byte (bool) – deprecated
-
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’
-
display_data
(trans, data, preview=False, filename=None, to_ext=None, **kwd)[source]¶ Displays data in central pane if preview is True, else handles download.
Datatypes should be very careful if overridding this method and this interface between datatypes and Galaxy will likely change.
TOOD: Document alternatives to overridding this method (data providers?).
-
repair_methods
(dataset)[source]¶ Unimplemented method, returns dict with method/option for repairing errors
-
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)
-
as_display_type
(dataset, type, **kwd)[source]¶ Returns modified file contents for a particular display type
-
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.
-
get_converter_types
(original_dataset, datatypes_registry)[source]¶ Returns available converters by type for this dataset
-
find_conversion_destination
(dataset, accepted_formats, datatypes_registry, **kwd)[source]¶ Returns ( target_ext, existing converted dataset )
-
convert_dataset
(trans, original_dataset, target_type, return_output=False, visible=True, deps=None, target_context=None, history=None)[source]¶ This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure.
-
after_setting_metadata
(dataset)[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.
-
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.
-
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.
-
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 0x7f482d4d28c0>, 'chunk': <function chunk_dataprovider at 0x7f482d4d2a28>, 'chunk64': <function chunk64_dataprovider at 0x7f482d4d2b90>}¶
-
-
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.
-
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.
-
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 0x7f482d4d28c0>, 'chunk': <function chunk_dataprovider at 0x7f482d4d2a28>, 'chunk64': <function chunk64_dataprovider at 0x7f482d4d2b90>, 'line': <function line_dataprovider at 0x7f482d4c01b8>, 'regex-line': <function regex_line_dataprovider at 0x7f482d4c0320>}¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.data.
Directory
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Data
Class representing a directory of files.
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf650>}¶
-
-
class
galaxy.datatypes.data.
GenericAsn1
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
Class for generic ASN.1 text format
-
edam_data
= 'data_0849'¶
-
edam_format
= 'format_1966'¶
-
file_ext
= 'asn1'¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf890>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bfad0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.data.
Newick
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
New Hampshire/Newick Format
-
edam_data
= 'data_0872'¶
-
edam_format
= 'format_1910'¶
-
file_ext
= 'newick'¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bfd50>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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'¶
-
edam_format
= 'format_1912'¶
-
file_ext
= 'nex'¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bffd0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
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 >>> def assert_peek_is(file_name, expected, *args, **kwd): ... path = get_test_fname(file_name) ... peek = get_file_peek(path, *args, **kwd) ... assert peek == expected, "%s != %s" % (peek, expected) >>> assert_peek_is('0_nonewline', u'0') >>> assert_peek_is('0.txt', u'0\n') >>> assert_peek_is('4.bed', u'chr22\t30128507\t31828507\tuc003bnx.1_cds_2_0_chr22_29227_f\t0\t+\n', LINE_COUNT=1) >>> assert_peek_is('1.bed', u'chr1\t147962192\t147962580\tCCDS989.1_cds_0_0_chr1_147962193_r\t0\t-\nchr1\t147984545\t147984630\tCCDS990.1_cds_0_0_chr1_147984546_f\t0\t+\n', LINE_COUNT=2)
galaxy.datatypes.genetics module¶
rgenetics datatypes Use at your peril Ross Lazarus for the rgenetics and galaxy projects
genome graphs datatypes derived from Interval datatypes genome graphs datasets have a header row with appropriate columnames The first column is always the marker - eg columname = rs, first row= rs12345 if the rows are snps subsequent row values are all numeric ! Will fail if any non numeric (eg ‘+’ or ‘NA’) values ross lazarus for rgenetics august 20 2007
-
class
galaxy.datatypes.genetics.
GenomeGraphs
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
Tab delimited data containing a marker id and any number of numeric values
-
file_ext
= 'gg'¶
-
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
-
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
-
metadata_spec
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805780fd0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805780190>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'markerCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805780210>}¶
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805780d50>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805780890>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805780ed0>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48057801d0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805780950>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805780490>}¶
-
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804430d50>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805780810>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805780110>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805780910>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805780ad0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804430550>}¶
-
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48044305d0>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804430690>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804430e90>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804430c90>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804430a90>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804430cd0>}¶
-
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804430a10>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.genetics.
SNPMatrix
(**kwd)[source]¶ Bases:
galaxy.datatypes.genetics.Rgenetics
BioC SNPMatrix Rgenetics data collections
-
file_ext
= 'snpmatrix'¶
-
metadata_spec
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804430b10>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.genetics.
Lped
(**kwd)[source]¶ Bases:
galaxy.datatypes.genetics.Rgenetics
linkage pedigree (ped,map) Rgenetics data collections
-
file_ext
= 'lped'¶
-
metadata_spec
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804f42c50>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804f42510>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804f42cd0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.genetics.
Phe
(**kwd)[source]¶ Bases:
galaxy.datatypes.genetics.Rgenetics
Phenotype file
-
file_ext
= 'phe'¶
-
metadata_spec
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804f42050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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
-
file_ext
= 'fped'¶
-
metadata_spec
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804f42190>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804f42ad0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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'¶
-
metadata_spec
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48042505d0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804250d10>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804250a10>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.genetics.
Snptest
(**kwd)[source]¶ Bases:
galaxy.datatypes.genetics.Rgenetics
BioC snptest Rgenetics data collections
-
file_ext
= 'snptest'¶
-
metadata_spec
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804250f90>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804250250>, 'chrom_bed': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804250710>, 'chrom_windows': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804250c50>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'input_config': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804250ad0>, 'tmp_archive': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48042503d0>}¶
-
-
class
galaxy.datatypes.genetics.
Pheno
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
base class for pheno files
-
file_ext
= 'pheno'¶
-
metadata_spec
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804e7b450>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804e7bd90>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804e7b390>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804e7b9d0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804e7b5d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804e7b310>}¶
-
-
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 :)
-
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)
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804e7b250>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804e7bb50>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804e7b7d0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'pheCols': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804e7b410>, 'pheno_path': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804e7bfd0>}¶
-
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48055db750>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48055db090>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4804e7bf90>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'pheCols': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48055dbfd0>, 'pheno_path': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48055dba50>}¶
-
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48055dbb10>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48055db050>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48055dbbd0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'pheCols': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48055dbc50>, 'pheno_path': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48055db450>}¶
-
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48055db4d0>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48055dbe50>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48055db350>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'pheCols': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48055dbf10>, 'pheno_path': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805b8a910>}¶
-
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805b8aa90>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805b8af10>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805b8a210>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805b8a0d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4805b8a990>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
sniff
(filename)¶
-
galaxy.datatypes.gis module¶
GIS classes
-
class
galaxy.datatypes.gis.
Shapefile
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
The Shapefile data format: For more information please see http://en.wikipedia.org/wiki/Shapefile
-
composite_type
= 'auto_primary_file'¶
-
file_ext
= 'shp'¶
-
allow_datatype_change
= False¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48028dec50>}¶
-
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 0x7f482d4d28c0>, 'chunk': <function chunk_dataprovider at 0x7f482d4d2a28>, 'chunk64': <function chunk64_dataprovider at 0x7f482d4d2b90>, 'line': <function line_dataprovider at 0x7f482d4c01b8>, 'node-edge': <function node_edge_dataprovider at 0x7f48028cfc80>, 'regex-line': <function regex_line_dataprovider at 0x7f482d4c0320>, 'xml': <function xml_dataprovider at 0x7f48067fdde8>}¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48018a9f10>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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 0x7f482d4d28c0>, 'chunk': <function chunk_dataprovider at 0x7f482d4d2a28>, 'chunk64': <function chunk64_dataprovider at 0x7f482d4d2b90>, 'column': <function column_dataprovider at 0x7f482a5bc938>, 'dataset-column': <function dataset_column_dataprovider at 0x7f482a5bcaa0>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7f482a5bcd70>, 'dict': <function dict_dataprovider at 0x7f482a5bcc08>, 'line': <function line_dataprovider at 0x7f482d4c01b8>, 'node-edge': <function node_edge_dataprovider at 0x7f48019df140>, 'regex-line': <function regex_line_dataprovider at 0x7f482d4c0320>}¶
-
metadata_spec
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48019e5450>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48019e53d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48019e5350>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48019e5250>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48019e52d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48019e54d0>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480289c790>}¶
-
-
class
galaxy.datatypes.images.
Jpg
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3579'¶
-
file_ext
= 'jpg'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480289ca90>}¶
-
-
class
galaxy.datatypes.images.
Png
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3603'¶
-
file_ext
= 'png'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480289c7d0>}¶
-
-
class
galaxy.datatypes.images.
Tiff
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3591'¶
-
file_ext
= 'tiff'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480289cf50>}¶
-
-
class
galaxy.datatypes.images.
Hamamatsu
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
file_ext
= 'vms'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480289c990>}¶
-
-
class
galaxy.datatypes.images.
Mirax
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
file_ext
= 'mrxs'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480289c750>}¶
-
-
class
galaxy.datatypes.images.
Sakura
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
file_ext
= 'svslide'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48019e5a10>}¶
-
-
class
galaxy.datatypes.images.
Nrrd
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
file_ext
= 'nrrd'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48019e5910>}¶
-
-
class
galaxy.datatypes.images.
Bmp
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3592'¶
-
file_ext
= 'bmp'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48019e58d0>}¶
-
-
class
galaxy.datatypes.images.
Gif
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3467'¶
-
file_ext
= 'gif'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48019e55d0>}¶
-
-
class
galaxy.datatypes.images.
Im
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3593'¶
-
file_ext
= 'im'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48019e5dd0>}¶
-
-
class
galaxy.datatypes.images.
Pcd
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3594'¶
-
file_ext
= 'pcd'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802107d50>}¶
-
-
class
galaxy.datatypes.images.
Pcx
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3595'¶
-
file_ext
= 'pcx'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480189a290>}¶
-
-
class
galaxy.datatypes.images.
Ppm
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3596'¶
-
file_ext
= 'ppm'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480189a150>}¶
-
-
class
galaxy.datatypes.images.
Psd
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3597'¶
-
file_ext
= 'psd'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480189a8d0>}¶
-
-
class
galaxy.datatypes.images.
Xbm
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3598'¶
-
file_ext
= 'xbm'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480189d290>}¶
-
-
class
galaxy.datatypes.images.
Xpm
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3599'¶
-
file_ext
= 'xpm'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480189d4d0>}¶
-
-
class
galaxy.datatypes.images.
Rgb
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3600'¶
-
file_ext
= 'rgb'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480189d250>}¶
-
-
class
galaxy.datatypes.images.
Pbm
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3601'¶
-
file_ext
= 'pbm'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48035a1090>}¶
-
-
class
galaxy.datatypes.images.
Pgm
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3602'¶
-
file_ext
= 'pgm'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48035a1290>}¶
-
-
class
galaxy.datatypes.images.
Eps
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3466'¶
-
file_ext
= 'eps'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48035a1490>}¶
-
-
class
galaxy.datatypes.images.
Rast
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3605'¶
-
file_ext
= 'rast'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48035a1690>}¶
-
-
class
galaxy.datatypes.images.
Pdf
(**kwd)[source]¶ Bases:
galaxy.datatypes.images.Image
-
edam_format
= 'format_3508'¶
-
file_ext
= 'pdf'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48035a18d0>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48035a1ad0>}¶
-
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48035a1d10>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.images.
Laj
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
Class describing a LAJ Applet
-
file_ext
= 'laj'¶
-
copy_safe_peek
= False¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48035a1f50>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
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 0x7f482d4d28c0>, 'chunk': <function chunk_dataprovider at 0x7f482d4d2a28>, 'chunk64': <function chunk64_dataprovider at 0x7f482d4d2b90>, 'column': <function column_dataprovider at 0x7f482a5bc938>, 'dataset-column': <function dataset_column_dataprovider at 0x7f482a5bcaa0>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7f482a5bcd70>, 'dict': <function dict_dataprovider at 0x7f482a5bcc08>, 'genomic-region': <function genomic_region_dataprovider at 0x7f482a56c050>, 'genomic-region-dict': <function genomic_region_dict_dataprovider at 0x7f482a56c1b8>, 'interval': <function interval_dataprovider at 0x7f482a56c320>, 'interval-dict': <function interval_dict_dataprovider at 0x7f482a56c488>, 'line': <function line_dataprovider at 0x7f482d4c01b8>, 'regex-line': <function regex_line_dataprovider at 0x7f482d4c0320>}¶
-
metadata_spec
= {'chromCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d290>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d510>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'endCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d390>, 'nameCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d490>, 'startCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d310>, 'strandCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d410>}¶
-
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
= {'chromCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d750>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d9d0>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'endCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d850>, 'nameCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d950>, 'startCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d7d0>, 'strandCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d8d0>}¶
-
-
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( 'interv1.bed' ) >>> Bed().sniff( fname ) True >>> fname = get_test_fname( 'complete.bed' ) >>> Bed().sniff( fname ) True
-
metadata_spec
= {'chromCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56dc50>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56de50>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'endCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56dd50>, 'nameCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d490>, 'startCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56dcd0>, 'strandCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56ddd0>, 'viz_filter_cols': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56ded0>}¶
-
-
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
= {'chromCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a571150>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a571350>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'endCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a571250>, 'nameCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d490>, 'startCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5711d0>, 'strandCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5712d0>, 'viz_filter_cols': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5713d0>}¶
-
-
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
= {'chromCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a571650>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5718d0>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'endCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a571750>, 'nameCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a571850>, 'startCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5716d0>, 'strandCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5717d0>, 'viz_filter_cols': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56ded0>}¶
-
-
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
= {'chromCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a571b10>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a571d90>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'endCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a571c10>, 'nameCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a571d10>, 'startCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a571b90>, 'strandCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a571c90>, 'viz_filter_cols': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56ded0>}¶
-
-
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
= {'chromCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a571fd0>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a290>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'endCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a110>, 'nameCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a210>, 'startCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a090>, 'strandCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a190>, 'viz_filter_cols': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56ded0>}¶
-
-
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.gff3') >>> Gff().sniff( fname ) False >>> fname = get_test_fname('test.gff') >>> Gff().sniff( fname ) True
-
dataproviders
= {'base': <function base_dataprovider at 0x7f482d4d28c0>, 'chunk': <function chunk_dataprovider at 0x7f482d4d2a28>, 'chunk64': <function chunk64_dataprovider at 0x7f482d4d2b90>, 'column': <function column_dataprovider at 0x7f482a5bc938>, 'dataset-column': <function dataset_column_dataprovider at 0x7f482a5bcaa0>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7f482a5bcd70>, 'dict': <function dict_dataprovider at 0x7f482a5bcc08>, 'genomic-region': <function genomic_region_dataprovider at 0x7f482a5758c0>, 'genomic-region-dict': <function genomic_region_dict_dataprovider at 0x7f482a575a28>, 'interval': <function interval_dataprovider at 0x7f482a575b90>, 'interval-dict': <function interval_dict_dataprovider at 0x7f482a575cf8>, 'line': <function line_dataprovider at 0x7f482d4c01b8>, 'regex-line': <function regex_line_dataprovider at 0x7f482d4c0320>}¶
-
metadata_spec
= {'attribute_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a890>, 'attributes': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a810>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a790>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a710>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>}¶
-
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.gff3') >>> Gff3().sniff( fname ) True
-
metadata_spec
= {'attribute_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a890>, 'attributes': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a810>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57ab10>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a710>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>}¶
-
-
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
= {'attribute_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a890>, 'attributes': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57a810>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57add0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a57ad50>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>}¶
-
-
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( 'interv1.bed' ) >>> Wiggle().sniff( fname ) False >>> fname = get_test_fname( 'wiggle.wig' ) >>> Wiggle().sniff( fname ) True
-
dataproviders
= {'base': <function base_dataprovider at 0x7f482d4d28c0>, 'chunk': <function chunk_dataprovider at 0x7f482d4d2a28>, 'chunk64': <function chunk64_dataprovider at 0x7f482d4d2b90>, 'column': <function column_dataprovider at 0x7f482a5bc938>, 'dataset-column': <function dataset_column_dataprovider at 0x7f482a5bcaa0>, 'dataset-dict': <function dataset_dict_dataprovider at 0x7f482a5bcd70>, 'dict': <function dict_dataprovider at 0x7f482a5bcc08>, 'line': <function line_dataprovider at 0x7f482d4c01b8>, 'regex-line': <function regex_line_dataprovider at 0x7f482d4c0320>, 'wiggle': <function wiggle_dataprovider at 0x7f482a57f9b0>, 'wiggle-dict': <function wiggle_dict_dataprovider at 0x7f482a57fb18>}¶
-
metadata_spec
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584150>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>}¶
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5845d0>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584550>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5844d0>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5843d0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584450>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584650>}¶
-
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
= {'chromCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584890>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584a90>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'endCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584990>, 'nameCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d490>, 'startCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584910>, 'strandCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584a10>}¶
-
-
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
= {'chrom1Col': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584cd0>, 'chrom2Col': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584e50>, 'chromCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d290>, 'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a4ce090>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'end1Col': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584dd0>, 'end2Col': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584f50>, 'endCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d390>, 'nameCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d490>, 'start1Col': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584d50>, 'start2Col': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584ed0>, 'startCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d310>, 'strandCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a56d410>, 'valueCol': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a584fd0>}¶
-
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a4ce350>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a4ce2d0>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>}¶
-
sniff
(filename)¶
-
file_ext
= 'scidx'¶
-
galaxy.datatypes.isa module¶
ISA datatype
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
¶
-
requires_dataset_id
¶
-
-
class
galaxy.datatypes.metadata.
MetadataSpecCollection
(*args, **kwds)[source]¶ Bases:
collections.OrderedDict
A simple extension of OrderedDict 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.
-
galaxy.datatypes.microarrays module¶
-
class
galaxy.datatypes.microarrays.
GenericMicroarrayFile
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
Abstract class for most of the microarray files.
-
metadata_spec
= {'block_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490310>, 'block_type': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490390>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'file_format': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490110>, 'file_type': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490290>, 'number_of_data_columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490210>, 'number_of_optional_header_records': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490190>, 'version_number': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490090>}¶
-
-
class
galaxy.datatypes.microarrays.
Gal
(**kwd)[source]¶ Bases:
galaxy.datatypes.microarrays.GenericMicroarrayFile
Gal File format described at: http://mdc.custhelp.com/app/answers/detail/a_id/18883/#gal
-
edam_format
= 'format_3829'¶
-
edam_data
= 'data_3110'¶
-
file_ext
= 'gal'¶
-
sniff_prefix
(file_prefix)[source]¶ Try to guess if the file is a Gal file. >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname(‘test.gal’) >>> Gal().sniff(fname) True >>> fname = get_test_fname(‘test.gpr’) >>> Gal().sniff(fname) False
-
metadata_spec
= {'block_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490750>, 'block_type': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48014907d0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'file_format': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490550>, 'file_type': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48014906d0>, 'number_of_data_columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490650>, 'number_of_optional_header_records': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48014905d0>, 'version_number': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48014904d0>}¶
-
sniff
(filename)¶
-
-
class
galaxy.datatypes.microarrays.
Gpr
(**kwd)[source]¶ Bases:
galaxy.datatypes.microarrays.GenericMicroarrayFile
Gpr File format described at: http://mdc.custhelp.com/app/answers/detail/a_id/18883/#gpr
-
edam_format
= 'format_3829'¶
-
edam_data
= 'data_3110'¶
-
file_ext
= 'gpr'¶
-
sniff_prefix
(file_prefix)[source]¶ Try to guess if the file is a Gpr file. >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname(‘test.gpr’) >>> Gpr().sniff(fname) True >>> fname = get_test_fname(‘test.gal’) >>> Gpr().sniff(fname) False
-
metadata_spec
= {'block_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490b90>, 'block_type': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490c10>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'file_format': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490990>, 'file_type': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490b10>, 'number_of_data_columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490a90>, 'number_of_optional_header_records': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490a10>, 'version_number': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801490910>}¶
-
sniff
(filename)¶
-
galaxy.datatypes.molecules module¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_molecules': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801354890>}¶
-
-
class
galaxy.datatypes.molecules.
MOL
(**kwd)[source]¶ Bases:
galaxy.datatypes.molecules.GenericMolFile
-
file_ext
= 'mol'¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_molecules': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48013541d0>}¶
-
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_molecules': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801381d10>}¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_molecules': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801381950>}¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_molecules': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801381150>}¶
-
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.
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801483d10>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5e1990>}¶
-
-
class
galaxy.datatypes.molecules.
DRF
(**kwd)[source]¶ Bases:
galaxy.datatypes.molecules.GenericMolFile
-
file_ext
= 'drf'¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_molecules': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801483610>}¶
-
-
class
galaxy.datatypes.molecules.
PHAR
(**kwd)[source]¶ Bases:
galaxy.datatypes.molecules.GenericMolFile
Pharmacophore database format from silicos-it.
-
file_ext
= 'phar'¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_molecules': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480171e390>}¶
-
-
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
= {'chain_ids': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480160d2d0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_molecules': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801354890>}¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_molecules': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480160d9d0>}¶
-
sniff
(filename)¶
-
-
class
galaxy.datatypes.molecules.
PQR
(**kwd)[source]¶ Bases:
galaxy.datatypes.molecules.GenericMolFile
Protein Databank format. https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html
-
file_ext
= 'pqr'¶
-
get_matcher
()[source]¶ - Atom and HETATM line fields are space separated, match group:
- 0: Field_name
- A string which specifies the type of PQR entry: ATOM or HETATM.
- 1: Atom_number
- An integer which provides the atom index.
- 2: Atom_name
- A string which provides the atom name.
- 3: Residue_name
- A string which provides the residue name.
- 5: Chain_ID (Optional, group 4 is whole field)
- An optional string which provides the chain ID of the atom. Note that chain ID support is a new feature of APBS 0.5.0 and later versions.
- 6: Residue_number
- An integer which provides the residue index.
- 7: X 8: Y 9: Z
- 3 floats which provide the atomic coordinates (in angstroms)
- 10: Charge
- A float which provides the atomic charge (in electrons).
- 11: Radius
- A float which provides the atomic radius (in angstroms).
-
sniff_prefix
(file_prefix)[source]¶ Try to guess if the file is a PQR file. >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname(‘5e5z.pqr’) >>> PQR().sniff(fname) True >>> fname = get_test_fname(‘drugbank_drugs.cml’) >>> PQR().sniff(fname) False
-
metadata_spec
= {'chain_ids': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480160dc50>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_molecules': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4801354890>}¶
-
sniff
(filename)¶
-
-
class
galaxy.datatypes.molecules.
grd
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
-
file_ext
= 'grd'¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480160ded0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.molecules.
grdtgz
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
-
file_ext
= 'grd.tgz'¶
-
metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480138a190>}¶
-
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480138a490>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480138a410>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'number_of_molecules': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480138a510>}¶
-
sniff
(filename)¶
-
-
class
galaxy.datatypes.molecules.
SMILES
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'smi'¶
-
column_names
= ['SMILES', 'TITLE']¶
-
metadata_spec
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480138a810>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480138a790>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'number_of_molecules': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480138a890>}¶
-
-
class
galaxy.datatypes.molecules.
CML
(**kwd)[source]¶ Bases:
galaxy.datatypes.xml.GenericXml
Chemical Markup Language http://cml.sourceforge.net/
-
file_ext
= 'cml'¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4831510f10>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_molecules': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480138ab10>}¶
-
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
= {'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cad4d0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'labels': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cad550>, 'otulabels': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cad5d0>}¶
-
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
= {'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cad710>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'labels': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cad790>, 'otulabels': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cad810>}¶
-
-
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
= {'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cad4d0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'groups': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cad950>, 'labels': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cad550>, 'otulabels': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cad5d0>}¶
-
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cadc90>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cadc10>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cadb90>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cada90>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cadb10>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cadd10>}¶
-
sniff
(filename)¶
-
-
class
galaxy.datatypes.mothur.
AlignCheck
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.align.check'¶
-
metadata_spec
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbc090>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cadfd0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cadf50>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cade50>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800caded0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbc110>}¶
-
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbc450>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbc3d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbc350>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbc250>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbc2d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbc4d0>}¶
-
-
class
galaxy.datatypes.mothur.
DistanceMatrix
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
-
file_ext
= 'mothur.dist'¶ Add metadata elements
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'sequence_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbc610>}¶
-
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'sequence_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbc750>}¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'sequence_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbc890>}¶
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1150>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'sequence_count': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbc9d0>}¶
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbcd10>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbcc90>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbcc10>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbcb10>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbcb90>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbcd90>}¶
-
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc9150>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc90d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc9050>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbcf10>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cbcf90>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc91d0>}¶
-
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1150>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'groups': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc9410>}¶
-
-
class
galaxy.datatypes.mothur.
AccNos
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.accnos'¶
-
metadata_spec
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc9850>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc97d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc9750>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc9650>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc96d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc98d0>}¶
-
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc9b10>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc9f50>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc9ed0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc9e50>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc9d50>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc9dd0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800cc9fd0>}¶
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1150>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'filtered': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4d210>, 'masked': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4d290>}¶
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4d4d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1150>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'groups': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4d6d0>}¶
-
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4db10>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4da90>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4da10>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4d910>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4d990>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4db90>}¶
-
sniff
(filename)¶
-
-
class
galaxy.datatypes.mothur.
ConsensusTaxonomy
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.cons.taxonomy'¶
-
metadata_spec
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4dfd0>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4df50>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4ded0>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4ddd0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b4de50>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b56090>}¶
-
-
class
galaxy.datatypes.mothur.
TaxonomySummary
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
-
file_ext
= 'mothur.tax.summary'¶
-
metadata_spec
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b564d0>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b56450>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b563d0>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b562d0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b56350>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b56550>}¶
-
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b56990>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b56910>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b56890>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b56790>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b56810>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b56a10>}¶
-
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
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1150>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'flow_order': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b56d10>, 'flow_values': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800b56c90>}¶
-
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
= {'cm_version': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480059d390>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_models': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480059d310>}¶
-
sniff
(filename)¶
-
-
class
galaxy.datatypes.msa.
Hmmer
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
-
edam_data
= 'data_1364'¶
-
edam_format
= 'format_1370'¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480059d4d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
sniff
(filename)¶
-
-
class
galaxy.datatypes.msa.
Hmmer2
(**kwd)[source]¶ Bases:
galaxy.datatypes.msa.Hmmer
-
edam_format
= 'format_3328'¶
-
file_ext
= 'hmm2'¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480059d610>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
class
galaxy.datatypes.msa.
Hmmer3
(**kwd)[source]¶ Bases:
galaxy.datatypes.msa.Hmmer
-
edam_format
= 'format_3329'¶
-
file_ext
= 'hmm3'¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480059d710>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480059d850>}¶
-
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_models': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480059d990>}¶
-
sniff
(filename)¶
-
-
class
galaxy.datatypes.msa.
MauveXmfa
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
-
file_ext
= 'xmfa'¶
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'number_of_models': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480059db50>}¶
-
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
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800557b50>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800557c50>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
-
-
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
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800557b50>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'neostore_zip': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800557e10>, 'reference_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800557d90>}¶
-
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
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48003d6690>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'sequence_space': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480040e850>}¶
-
-
class
galaxy.datatypes.ngsindex.
BowtieColorIndex
(**kwd)[source]¶ Bases:
galaxy.datatypes.ngsindex.BowtieIndex
Bowtie color space index
-
file_ext
= 'bowtie_color_index'¶
-
metadata_spec
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48003d6690>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'sequence_space': <galaxy.model.metadata.MetadataElementSpec object at 0x7f480040e2d0>}¶
-
-
class
galaxy.datatypes.ngsindex.
BowtieBaseIndex
(**kwd)[source]¶ Bases:
galaxy.datatypes.ngsindex.BowtieIndex
Bowtie base space index
-
file_ext
= 'bowtie_base_index'¶
-
metadata_spec
= {'base_name': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48003d6690>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4802c38ed0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'sequence_space': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800689710>}¶
-
galaxy.datatypes.phylip module¶
Created on January. 05, 2018
@authors: Kenzo-Hugo Hillion and Fabien Mareuil, Institut Pasteur, Paris @contacts: kehillio@pasteur.fr and fabien.mareuil@pasteur.fr @project: galaxy @githuborganization: C3BI Phylip datatype sniffer
-
class
galaxy.datatypes.phylip.
Phylip
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
Phylip format stores a multiple sequence alignment
-
edam_data
= 'data_0863'¶
-
edam_format
= 'format_1997'¶
-
file_ext
= 'phylip'¶ Add metadata elements
-
set_meta
(dataset, **kwd)[source]¶ Set the number of sequences and the number of data lines in dataset.
-
metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf3d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'sequences': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800475410>}¶
-
sniff
(filename)¶
-
galaxy.datatypes.plant_tribes module¶
-
class
galaxy.datatypes.plant_tribes.
Smat
(**kwd)[source]¶ Bases:
galaxy.datatypes.data.Text
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file_ext
= 'smat'¶
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sniff_prefix
(file_prefix)[source]¶ The use of ESTScan implies the creation of scores matrices which reflect the codons preferences in the studied organisms. The ESTScan package includes scripts for generating these files. The output of these scripts consists of the matrices, one for each isochor, and which look like this:
FORMAT: hse_4is.conf CODING REGION 6 3 1 s C+G: 0 44 -1 0 2 -2 2 1 -8 0
>>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname('test_space.txt') >>> Smat().sniff(fname) False >>> fname = get_test_fname('test_tab.bed') >>> Smat().sniff(fname) False >>> fname = get_test_fname('1.smat') >>> Smat().sniff(fname) True
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metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f4800320350>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
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sniff
(filename)¶
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class
galaxy.datatypes.plant_tribes.
PlantTribesKsComponents
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
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file_ext
= 'ptkscmp'¶
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set_meta
(dataset, **kwd)[source]¶ Set the number of significant components in the Ks distribution. The dataset will always be on the order of less than 10 lines.
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sniff
(filename)[source]¶ >>> from galaxy.datatypes.sniff import get_test_fname >>> fname = get_test_fname('test_tab.bed') >>> PlantTribesKsComponents().sniff(fname) False >>> fname = get_test_fname('1.ptkscmp') >>> PlantTribesKsComponents().sniff(fname) True
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metadata_spec
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1250>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c11d0>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1150>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c1050>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c10d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482a5c12d0>, 'number_comp': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48003205d0>}¶
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galaxy.datatypes.proteomics module¶
Proteomics Datatypes
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class
galaxy.datatypes.proteomics.
Wiff
(**kwd)[source]¶ Bases:
galaxy.datatypes.binary.Binary
Class for wiff files.
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edam_data
= 'data_2536'¶
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edam_format
= 'format_3710'¶
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file_ext
= 'wiff'¶
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allow_datatype_change
= False¶
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composite_type
= 'auto_primary_file'¶
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metadata_spec
= {'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d60d0>}¶
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class
galaxy.datatypes.proteomics.
PepXmlReport
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
pepxml converted to tabular report
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edam_data
= 'data_2536'¶
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file_ext
= 'pepxml.tsv'¶
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metadata_spec
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d6510>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d6490>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d6410>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d6310>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d6390>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d6590>}¶
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class
galaxy.datatypes.proteomics.
ProtXmlReport
(**kwd)[source]¶ Bases:
galaxy.datatypes.tabular.Tabular
protxml converted to tabular report
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edam_data
= 'data_2536'¶
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file_ext
= 'protxml.tsv'¶
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comment_lines
= 1¶
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metadata_spec
= {'column_names': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d69d0>, 'column_types': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d6950>, 'columns': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d68d0>, 'comment_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d67d0>, 'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d6850>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>, 'delimiter': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d6a50>}¶
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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.
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edam_data
= 'data_2536'¶
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edam_format
= 'format_2032'¶
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metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d6cd0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
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class
galaxy.datatypes.proteomics.
PepXml
(**kwd)[source]¶ Bases:
galaxy.datatypes.proteomics.ProteomicsXml
pepXML data
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edam_format
= 'format_3655'¶
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file_ext
= 'pepxml'¶
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blurb
= 'pepXML data'¶
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root
= 'msms_pipeline_analysis'¶
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metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d6f10>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
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class
galaxy.datatypes.proteomics.
MzML
(**kwd)[source]¶ Bases:
galaxy.datatypes.proteomics.ProteomicsXml
mzML data
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edam_format
= 'format_3244'¶
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file_ext
= 'mzml'¶
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blurb
= 'mzML Mass Spectrometry data'¶
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root
= '(mzML|indexedmzML)'¶
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metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d8190>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
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class
galaxy.datatypes.proteomics.
NmrML
(**kwd)[source]¶ Bases:
galaxy.datatypes.proteomics.ProteomicsXml
nmrML data
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file_ext
= 'nmrml'¶
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blurb
= 'nmrML NMR data'¶
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root
= 'nmrML'¶
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metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d83d0>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
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class
galaxy.datatypes.proteomics.
ProtXML
(**kwd)[source]¶ Bases:
galaxy.datatypes.proteomics.ProteomicsXml
protXML data
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file_ext
= 'protxml'¶
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blurb
= 'prot XML Search Results'¶
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root
= 'protein_summary'¶
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metadata_spec
= {'data_lines': <galaxy.model.metadata.MetadataElementSpec object at 0x7f48001d8610>, 'dbkey': <galaxy.model.metadata.MetadataElementSpec object at 0x7f482d4bf110>}¶
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class
galaxy.datatypes.proteomics.
MzXML
(**kwd)[source]¶ Bases:
galaxy.datatypes.proteomics.ProteomicsXml
mzXML data