Read GPA 1.0 format files (PRIVATE).

This iterator is used to read a gp_association.* file which is in the GPA 1.0 format. Do not call directly. Rather, use the gpaiterator function.

Read GPA 1.1 format files (PRIVATE).

This iterator is used to read a gp_association.goa_uniprot file which is in the GPA 1.1 format. Do not call directly. Rather use the gpa_iterator function

Read GPI 1.0 format files (PRIVATE).

This iterator is used to read a gp_information.goa_uniprot file which is in the GPI 1.0 format.

Read GPI 1.0 format files (PRIVATE).

This iterator is used to read a gp_information.goa_uniprot file which is in the GPI 1.0 format.

Iterates 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

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']

Wrapper function: 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

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.

Accepts 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.

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

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.