# 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

Gene Association File, GAF formats: http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/ http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/ http://geneontology.org/docs/go-annotation-file-gaf-format-2.0/

Gene Product Association Data (GPA format) README: http://geneontology.org/docs/gene-product-association-data-gpad-format/

Gene Product Information (GPI format) README: http://geneontology.org/docs/gene-product-information-gpi-format/

Go Annotation files are located here: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/

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.x file.

  This function should be called to read a gene_association.goa_uniprot file. Reads the first record and returns a gaf 2.x or a gaf 1.0 iterator as needed

  Example: open, read, interat and filter results.

  Original data file has been trimmed 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=GAF20FIELDS)

  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=GAF20FIELDS)

  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.

Biopython v: 1.86

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