def test_write_hier_bp_mf_cc():
"""Test that write hierarchy writes all: BP, MF, CC"""
fin_anno = os.path.join(REPO, 'gene2go')
fin_dag = os.path.join(REPO, "go-basic.obo")
_dnld_anno(fin_anno)
#godag = get_godag(os.path.join(REPO, 'go-basic.obo'), loading_bar=None)
print('\nTEST STORING ONLY ONE SPECIES')
#### obj = Gene2GoReader(fin_anno)
godag = get_godag(fin_dag)
gene2gos = read_annotations(namespace='ALL')
tcntobj = TermCounts(godag, gene2gos) if gene2gos else None
gosubdag = GoSubDag(godag.keys(),
godag,
relationships=False,
tcntobj=tcntobj,
children=True,
prt=sys.stdout)
objwr = WrHierGO(gosubdag)
# 2020 11:
# 594,748 GO lines under GO:0008150
# 23,199 GO lines under GO:0003674
# 6,259 GO lines under GO:0005575
# 624,206 items WROTE: tmp_test_wr_hier_BP_MF_CC.txt
assert len(_wr_hier(['BP', 'MF', 'CC'], gosubdag.go2nt, objwr)) > 600000
assert len(_wr_hier([
'BP',
], gosubdag.go2nt, objwr)) > 500000
assert len(_wr_hier([
'MF',
], gosubdag.go2nt, objwr)) > 20000
assert len(_wr_hier([
'CC',
], gosubdag.go2nt, objwr)) > 5000
def test_semantic_i88():
"""Full set of annotations can be used to set TermCounts. No need to break it up."""
godag = get_godag("go-basic.obo")
# Associations
fin_gaf = os.path.join(REPO, "tair.gaf")
gene2gos_all = read_annotations(gaf=fin_gaf, namespace='ALL')
gene2gos_bp = read_annotations(gaf=fin_gaf, namespace='BP')
gene2gos_mf = read_annotations(gaf=fin_gaf, namespace='MF')
gene2gos_cc = read_annotations(gaf=fin_gaf, namespace='CC')
# Termcounts
prt = sys.stdout
termcounts_all = TermCounts(godag, gene2gos_all, prt=prt)
termcounts_bp = TermCounts(godag, gene2gos_bp, prt=prt)
termcounts_mf = TermCounts(godag, gene2gos_mf, prt=prt)
termcounts_cc = TermCounts(godag, gene2gos_cc, prt=prt)
# Test content in subset is the same as in the full GO counts
for goid, cnt in termcounts_bp.gocnts.items():
assert termcounts_all.gocnts[goid] == cnt
for goid, cnt in termcounts_mf.gocnts.items():
assert termcounts_all.gocnts[goid] == cnt
for goid, cnt in termcounts_cc.gocnts.items():
assert termcounts_all.gocnts[goid] == cnt
def __init__(self, args=None, prt=sys.stdout):
self.kws = DocOptParse(__doc__, self.kws_dct_all, self.kws_set_all).get_docargs(
args, intvals=set(['max_indent', 'dash_len']))
opt_attrs = OboOptionalAttrs.attributes.intersection(self.kws.keys())
godag = get_godag(self.kws['dag'], prt, optional_attrs=opt_attrs)
self.gene2gos = read_annotations(**self.kws)
self.tcntobj = TermCounts(godag, self.gene2gos) if self.gene2gos is not None else None
self.gosubdag = GoSubDag(godag.keys(), godag,
relationships='relationship' in opt_attrs,
tcntobj=self.tcntobj,
children=True,
prt=prt)
self.goids = self._init_goids()
self._adj_item_marks()
self._adj_include_only()
self._adj_for_assc()
def __init__(self, args=None, prt=sys.stdout):
self.kws = DocOptParse(__doc__, self.kws_dct_all, self.kws_set_all).get_docargs(
args, intvals=set(['max_indent', 'dash_len']))
opt_attrs = OboOptionalAttrs.attributes.intersection(self.kws.keys())
godag = get_godag(self.kws['dag'], prt, optional_attrs=opt_attrs)
self.gene2gos = read_annotations(**self.kws)
self.tcntobj = TermCounts(godag, self.gene2gos) if self.gene2gos is not None else None
self.gosubdag = GoSubDag(godag.keys(), godag,
relationships='relationship' in opt_attrs,
tcntobj=self.tcntobj,
children=True,
prt=prt)
self.goids = self._init_goids()
self._adj_item_marks()
self._adj_include_only()
self._adj_for_assc()