Bio.UniProt.GOA module

Parsers for the GAF, GPA and GPI formats from UniProt-GOA.

Uniprot-GOA README + GAF format description: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/README

GAF formats: http://www.geneontology.org/GO.format.annotation.shtml gp_association (GPA format) README: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gp_association_readme

gp_information (GPI format) README: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gp_information_readme

Bio.UniProt.GOA.gpi_iterator(handle)

Read GPI format files.

This function should be called to read a gp_information.goa_uniprot file. At the moment, there is only one format, but this may change, so this function is a placeholder a future wrapper.

Bio.UniProt.GOA.gpa_iterator(handle)

Read GPA format files.

This function should be called to read a gene_association.goa_uniprot file. Reads the first record and returns a gpa 1.1 or a gpa 1.0 iterator as needed

Bio.UniProt.GOA.gafbyproteiniterator(handle)

Iterate over records in a gene association file.

Returns a list of all consecutive records with the same DB_Object_ID This function should be called to read a gene_association.goa_uniprot file. Reads the first record and returns a gaf 2.0 or a gaf 1.0 iterator as needed 2016-04-09: added GAF 2.1 iterator & fixed bug in iterator assignment In the meantime GAF 2.1 uses the GAF 2.0 iterator

Bio.UniProt.GOA.gafiterator(handle)

Iterate over a GAF 1.0 or 2.0 file.

This function should be called to read a gene_association.goa_uniprot file. Reads the first record and returns a gaf 2.0 or a gaf 1.0 iterator as needed

Example: open, read, interat and filter results.

Original data file has been trimed to ~600 rows.

Original source ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/YEAST/goa_yeast.gaf.gz

>>> from Bio.UniProt.GOA import gafiterator, record_has
>>> Evidence = {'Evidence': set(['ND'])}
>>> Synonym = {'Synonym': set(['YA19A_YEAST', 'YAL019W-A'])}
>>> Taxon_ID = {'Taxon_ID': set(['taxon:559292'])}
>>> with open('UniProt/goa_yeast.gaf', 'r') as handle:
...     for rec in gafiterator(handle):
...         if record_has(rec, Taxon_ID) and record_has(rec, Evidence) and record_has(rec, Synonym):
...             for key in ('DB_Object_Name', 'Evidence', 'Synonym', 'Taxon_ID'):
...                 print(rec[key])
...
Putative uncharacterized protein YAL019W-A
ND
['YA19A_YEAST', 'YAL019W-A']
['taxon:559292']
Putative uncharacterized protein YAL019W-A
ND
['YA19A_YEAST', 'YAL019W-A']
['taxon:559292']
Putative uncharacterized protein YAL019W-A
ND
['YA19A_YEAST', 'YAL019W-A']
['taxon:559292']

Bio.UniProt.GOA.writerec(outrec, handle, fields=['DB', 'DB_Object_ID', 'DB_Object_Symbol', 'Qualifier', 'GO_ID', 'DB:Reference', 'Evidence', 'With', 'Aspect', 'DB_Object_Name', 'Synonym', 'DB_Object_Type', 'Taxon_ID', 'Date', 'Assigned_By', 'Annotation_Extension', 'Gene_Product_Form_ID'])

Write a single UniProt-GOA record to an output stream.

Caller should know the format version. Default: gaf-2.0 If header has a value, then it is assumed this is the first record, a header is written.

Bio.UniProt.GOA.writebyproteinrec(outprotrec, handle, fields=['DB', 'DB_Object_ID', 'DB_Object_Symbol', 'Qualifier', 'GO_ID', 'DB:Reference', 'Evidence', 'With', 'Aspect', 'DB_Object_Name', 'Synonym', 'DB_Object_Type', 'Taxon_ID', 'Date', 'Assigned_By', 'Annotation_Extension', 'Gene_Product_Form_ID'])

Write a list of GAF records to an output stream.

Caller should know the format version. Default: gaf-2.0 If header has a value, then it is assumed this is the first record, a header is written. Typically the list is the one read by fafbyproteinrec, which contains all consecutive lines with the same DB_Object_ID

Bio.UniProt.GOA.record_has(inrec, fieldvals)

Accept a record, and a dictionary of field values.

The format is {‘field_name’: set([val1, val2])}. If any field in the record has a matching value, the function returns True. Otherwise, returns False.