def read_gaf(fin_gaf, prt=sys.stdout, **kws):
"""Read Gene Association File (GAF). Return data."""
# keyword arguments what is read from GAF.
hdr_only = kws.get('hdr_only', None) # Read all data from GAF by default
# Read GAF file
gafobj = GafReader(fin_gaf, hdr_only, prt, **kws)
return gafobj.read_gaf(**kws)
def test_gaf_illegal(prt=sys.stdout):
"""Test finding and reporting illegal GAF lines seen in the field."""
fin_gaf = os.path.join(REPO, 'data/gaf/goa_human_illegal.gaf')
gafobj = GafReader(fin_gaf, hdr_only=False, prt=prt)
id2gos = gafobj.read_gaf() # Read associations
assert len(id2gos) == 15, "IDS FOUND: EXP({E}) ACT({A})".format(
E=15, A=len(id2gos))
assert len(gafobj.datobj.ignored) == 1
assert len(gafobj.datobj.illegal_lines['ILLEGAL TAXON']) == 1
