def _get_objanno(fin_anno, anno_type=None, **kws):
"""Get association object"""
full_anno = os.path.join(REPO, fin_anno)
dnld_annofile(full_anno, anno_type)
obj = get_objanno(full_anno, anno_type, **kws)
if obj.name in {'gene2go', 'gaf'} or 'godag' in kws:
assert hasattr(obj.associations[0], 'NS')
# Check namespaces, if provided by the user
if 'namespaces' in kws:
_chk_namespaces(obj, kws['namespaces'])
return obj
def _get_objanno(fin_anno, anno_type=None, **kws):
"""Get association object"""
full_anno = os.path.join(REPO, fin_anno)
dnld_annofile(full_anno, anno_type)
obj = get_objanno(full_anno, anno_type, **kws)
if obj.name in {'gene2go', 'gaf'} or 'godag' in kws:
assert hasattr(obj.associations[0], 'NS')
# Check namespaces, if provided by the user
if 'namespaces' in kws:
_chk_namespaces(obj, kws['namespaces'])
return obj
def test_anno_read():
"""Test reading annotation file."""
fin_anno = os.path.join(REPO, 'goa_human.gaf')
dnld_annofile(fin_anno, 'gaf')
print('\nTEST STORING ONLY ONE SPECIES')
obj = GafReader(fin_anno)
obj.prt_summary_anno2ev()
## new = obj.read_gaf()
new = obj.get_id2gos_nss()
old = read_gaf(obj)
_prt_differences(new, old, obj)
print('{N} NEW'.format(N=len(new)))
print('{N} OLD'.format(N=len(old)))
assert len(new) == len(old), 'new({N}) != old({O})'.format(N=len(new), O=len(old))
print('\nTEST KWS: keep_ND and keep_NOT')
# pylint: disable=bad-whitespace
kws_lst = [
{'keep_ND': False, 'keep_NOT': False},
{'keep_ND': False, 'keep_NOT': True},
{'keep_ND': True, 'keep_NOT': False},
{'keep_ND': True, 'keep_NOT': True},
]
for kws in kws_lst:
print('\nTEST KWS:', kws)
## new = obj.read_gaf(namespace='BP', **kws)
new = obj.get_id2gos_nss(**kws)
old = read_gaf(obj, **kws)
_prt_differences(new, old, obj)
assert len(new) == len(old), 'new({N}) != old({O})'.format(N=len(new), O=len(old))
print('\nTEST GETTING REVERSE ASSOCIATIONS: GO2GENES')
## new = obj.read_gaf(go2geneids=True)
new = obj.get_id2gos_nss(go2geneids=True)
old = read_gaf(obj, go2geneids=True)
_prt_differences(new, old, obj)
assert len(new) == len(old), 'new({N}) != old({O})'.format(N=len(new), O=len(old))
print('\nTEST RETURNING ASSOCIATIONS FOR SELECTED EVIDENCE CODES')
evcodes = set(['ISO', 'IKR'])
print("\nTEST 9606 ev_include={CODES}".format(CODES=' '.join(evcodes)))
## new = obj.read_gaf(ev_include=evcodes)
new = obj.get_id2gos_nss(ev_include=evcodes)
old = read_gaf(obj, ev_include=evcodes)
_prt_differences(new, old, obj)
assert new == old
def test_i148_semsim_lin(prt=sys.stdout):
"""Test for issue 148, Lin Similarity if a term has no annotations"""
fin_gpad = os.path.join(REPO, 'goa_human.gpad')
dnld_annofile(fin_gpad, 'gpad')
godag = get_godag(os.path.join(REPO, "go-basic.obo"), loading_bar=None)
annoobj = GpadReader(fin_gpad, godag=godag)
goids = [
'GO:0042581', 'GO:0101002', 'GO:0042582', 'GO:0070820', 'GO:0008021',
'GO:0005766', 'GO:0016591'
]
associations = annoobj.get_id2gos('CC')
termcounts = TermCounts(godag, associations)
# Calculate Lin values
p2v = {
frozenset([a, b]): lin_sim(a, b, godag, termcounts)
for a, b in combo_w_rplc(goids, 2)
}
_prt_values(goids, p2v, prt=sys.stdout)
def _get_objanno(fin_anno, anno_type=None, **kws):
"""Get association object"""
full_anno = os.path.join(REPO, fin_anno)
dnld_annofile(full_anno, anno_type)
obj = get_objanno(full_anno, anno_type, **kws)
return obj
def test_anno_read():
"""Test reading annotation file."""
fin_anno = os.path.join(REPO, 'goa_human.gaf')
dnld_annofile(fin_anno, 'gaf')
print('\nTEST STORING ONLY ONE SPECIES')
obj = GafReader(fin_anno)
obj.prt_summary_anno2ev()
## new = obj.read_gaf()
new = obj.get_id2gos_nss()
old = read_gaf(obj)
_prt_differences(new, old, obj)
print('{N} NEW'.format(N=len(new)))
print('{N} OLD'.format(N=len(old)))
assert len(new) == len(old), 'new({N}) != old({O})'.format(N=len(new),
O=len(old))
print('\nTEST KWS: keep_ND and keep_NOT')
# pylint: disable=bad-whitespace
kws_lst = [
{
'keep_ND': False,
'keep_NOT': False
},
{
'keep_ND': False,
'keep_NOT': True
},
{
'keep_ND': True,
'keep_NOT': False
},
{
'keep_ND': True,
'keep_NOT': True
},
]
for kws in kws_lst:
print('\nTEST KWS:', kws)
## new = obj.read_gaf(namespace='BP', **kws)
new = obj.get_id2gos_nss(**kws)
old = read_gaf(obj, **kws)
_prt_differences(new, old, obj)
assert len(new) == len(old), 'new({N}) != old({O})'.format(N=len(new),
O=len(old))
print('\nTEST GETTING REVERSE ASSOCIATIONS: GO2GENES')
## new = obj.read_gaf(go2geneids=True)
new = obj.get_id2gos_nss(go2geneids=True)
old = read_gaf(obj, go2geneids=True)
_prt_differences(new, old, obj)
assert len(new) == len(old), 'new({N}) != old({O})'.format(N=len(new),
O=len(old))
print('\nTEST RETURNING ASSOCIATIONS FOR SELECTED EVIDENCE CODES')
evcodes = set(['ISO', 'IKR'])
print("\nTEST 9606 ev_include={CODES}".format(CODES=' '.join(evcodes)))
## new = obj.read_gaf(ev_include=evcodes)
new = obj.get_id2gos_nss(ev_include=evcodes)
old = read_gaf(obj, ev_include=evcodes)
_prt_differences(new, old, obj)
assert new == old
def get_objanno(fin_anno, anno_type=None, **kws):
"""Get association object"""
full_anno = os.path.join(REPO, fin_anno)
dnld_annofile(full_anno, anno_type)
obj = get_objanno(full_anno, anno_type, **kws)
return obj
