def test_missingsym():
"""Tests read a GAF with missing (required) DB_Symbol text."""
# Original gaf file (mgi.gaf) was reduced
fin_gaf = "tests/data/gaf_missingsym.mgi"
# Test that gene products that are missing the required DB_Symbol are ignored
gafobj = GafReader(fin_gaf, hdr_only=False)
assert not gafobj.chk_associations('gaf_missingsym.err')
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
# for ntd in gafobj.associations:
# print(ntd)
assert not gafobj.chk_associations('goa_human_illegal.err')
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
# for ntd in gafobj.associations:
# print(ntd)
assert not gafobj.chk_associations('goa_human_illegal.err')