goatools.anno.init.reader_gpad module

Read a Gene Product Association Data (GPAD) and store the data in a Python object. Annotations available from the Gene Ontology Consortium:

GPAD format:

http://geneontology.org/page/gene-product-association-data-gpad-format GPAD 2.0: https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md

class goatools.anno.init.reader_gpad.InitAssc(filename, godag)

Bases: object

Read annotation file and store a list of namedtuples.

gpadhdr = ['DB', 'DB_ID', 'Qualifier', 'GO_ID', 'DB_Reference', 'ECO', 'Evidence_Code', 'With_From', 'Taxon', 'Date', 'Assigned_By', 'Extension', 'Properties']

exp_numcol = 12

exp_qualifiers = {'NOT', 'acts_upstream_of', 'acts_upstream_of_negative_effect', 'acts_upstream_of_or_within', 'acts_upstream_of_or_within_negative_effect', 'acts_upstream_of_or_within_positive_effect', 'acts_upstream_of_positive_effect', 'colocalizes_with', 'contributes_to', 'enables', 'involved_in', 'is_active_in', 'located_in', 'part_of'}

relation2qualifier = {'BFO:0000050': 'part_of', 'RO:0001025': 'located_in', 'RO:0002263': 'acts_upstream_of', 'RO:0002264': 'acts_upstream_of_or_within', 'RO:0002325': 'colocalizes_with', 'RO:0002326': 'contributes_to', 'RO:0002327': 'enables', 'RO:0002331': 'involved_in', 'RO:0002432': 'is_active_in', 'RO:0004032': 'acts_upstream_of_or_within_positive_effect', 'RO:0004033': 'acts_upstream_of_or_within_negative_effect', 'RO:0004034': 'acts_upstream_of_positive_effect', 'RO:0004035': 'acts_upstream_of_negative_effect'}

cmpver = re.compile('^!gpad?-version:\\s*(\\S+)')

init_associations(hdr_only=False, namespaces=None, prt=sys.stdout)

Read GPAD file. HTTP address okay. GZIPPED/BZIPPED file okay.

class goatools.anno.init.reader_gpad.GpadHdr

Bases: object

Used to build a GPAD header.

cmpline = re.compile('^!(\\w[\\w\\s-]+:.*)$')

get_hdr()

Return GPAD header data as a string paragragh.

chkaddhdr(line)

If this line contains desired header info, save it.