def test_semantic_similarity(usr_assc=None):
"""Computing basic semantic similarities between GO terms."""
not_these = {'goa_uniprot_all.gaf', 'goa_uniprot_all_noiea.gaf'}
associations = sorted(ASSOCIATIONS.difference(not_these))
go2obj = get_go2obj()
# goids = go2obj.keys()
# http://current.geneontology.org/annotations/
if usr_assc is not None:
associations = [usr_assc]
not_found = set()
errs = []
for assc_name in associations: # Limit test numbers for speed
tic = timeit.default_timer()
# Get all the annotations from arabidopsis.
fin_gaf = os.path.join(REPO, assc_name)
if not os.path.exists(fin_gaf):
dnld_annotation(fin_gaf)
annoobj = GafReader(fin_gaf)
#### for nspc in ['BP', 'MF', 'CC']:
assc_gene2gos = annoobj.get_id2gos('all')
if not assc_gene2gos:
not_found.add(assc_name)
continue
# Calculate the information content of the single term, GO:0048364
# "Information content (GO:0048364) = 7.75481392334
# Initialize the counts of each GO term.
tcntobj = TermCounts(go2obj, assc_gene2gos)
go_cnt = tcntobj.gocnts.most_common()
#print tcntobj.gocnts.most_common()
if go_cnt:
print("{ASSC}".format(ASSC=assc_name))
print(tcntobj.aspect_counts)
gocnt_max = go_cnt[0][1]
prt_info(tcntobj, go_cnt, None)
prt_info(tcntobj, go_cnt, gocnt_max / 2.0)
prt_info(tcntobj, go_cnt, gocnt_max / 10.0)
print("{HMS} {hms} {ASSC}\n".format(ASSC=assc_name,
HMS=_hms(TIC),
hms=_hms(tic)))
print('{HMS} {N} Associations'.format(HMS=_hms(TIC), N=len(associations)))
if not_found:
_prt_not_found(not_found)
if errs:
fout_err = 'namespace_errors.txt'
with open(fout_err, 'w') as prt:
for err in errs:
prt.write(err)
print(' {N} ERRORS WROTE: {TXT}'.format(N=len(errs),
TXT=fout_err))
def test_i148b_semsim_lin(do_plt=False):
"""Test for issue 148, Lin Similarity if a term has no annotations"""
fin_gaf = os.path.join(REPO, 'tests/data/yangRWC/fig2a_nonleaf0.gaf')
godag = GODag(os.path.join(REPO, "tests/data/yangRWC/fig2a.obo"))
annoobj = GafReader(fin_gaf, godag=godag)
associations = annoobj.get_id2gos('CC')
tcntobj = TermCounts(godag, associations)
if do_plt:
_do_plt(tcntobj, godag)
goids = list(godag.keys())
##print(lin_sim('GO:0000006', 'GO:0000002', godag, tcntobj, 1.0))
## print(lin_sim('GO:0005575', 'GO:0005575', godag, tcntobj, 1.0))
##return
# Calculate Resnik values
p2r = {
frozenset([a, b]): resnik_sim(a, b, godag, tcntobj)
for a, b in combo_w_rplc(goids, 2)
}
_prt_values('Resnik', goids, p2r)
# Calculate Lin values
p2l = {
frozenset([a, b]): lin_sim(a, b, godag, tcntobj)
for a, b in combo_w_rplc(goids, 2)
}
_prt_values('Lin', goids, p2l)
_chk_lin(p2l)
return
# Calculate Resnik values
p2r = {
frozenset([a, b]): resnik_sim(a, b, godag, tcntobj)
for a, b in combo_w_rplc(goids, 2)
}
_prt_values('Resnik', goids, p2r)
# Calculate Lin values
p2l = {
frozenset([a, b]): lin_sim(a, b, godag, tcntobj)
for a, b in combo_w_rplc(goids, 2)
}
_prt_values('Lin', goids, p2l)
_chk_lin(p2l)
