def test_david_chart():
"""Read in a small obo, print list of GO terms and plot."""
repo = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")
david_dir = "{REPO}/data/gjoneska".format(REPO=repo)
ntobj = cx.namedtuple("david6p8", "TOTAL FDR Bonferroni Benjamini PValue")
# pylint: disable=bad-whitespace
fin2exp = {
"gjoneska2015_chart6p8_Consistent_Decrease.txt": ntobj._make([ 1773, 259, 249, 432, 1316]),
"gjoneska2015_chart6p8_Transient_Decrease.txt": ntobj._make([ 423, 0, 2, 2, 246]),
"gjoneska2015_chart6p8_Consistent_Increase.txt": ntobj._make([ 2359, 353, 308, 781, 1868]),
"gjoneska2015_chart6p8_Transient_Increase.txt": ntobj._make([ 2191, 658, 652, 1105, 1786]),
"gjoneska2015_chart6p8_Late_Decrease.txt": ntobj._make([ 2752, 591, 568, 1153, 2187]),
"gjoneska2015_chart6p8_Late_Increase.txt": ntobj._make([ 4597, 708, 616, 1715, 3603]),
}
tic = timeit.default_timer()
fin2obj = {f:DavidChartReader(os.path.join(david_dir, f)) for f in fin2exp.keys()}
prt_hms(tic, "Created DavidChartReader objects")
for fin, obj in fin2obj.items():
ntexp = fin2exp[fin]
assert ntexp.TOTAL == len(obj.nts)
obj.prt_num_sig()
ctr = obj.get_num_sig()
for fld, cnt_actual in ctr.most_common():
assert cnt_actual == getattr(ntexp, fld), "{FIN}: {FLD} Act({ACT}) Exp({EXP})".format(
FIN=fin, FLD=fld, ACT=cnt_actual, EXP=getattr(ntexp, fld))
def test_get_children(prt=sys.stdout):
"""Semantic Similarity test for Issue #86."""
# Load GO-DAG
fin_obo = "go-basic.obo"
repo = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")
godag = get_godag(os.path.join(repo, fin_obo))
go2obj = {go: o for go, o in godag.items() if go == o.id}
# Get all children for all GO IDs using get_all_children in GOTerm class
tic = timeit.default_timer()
go2children_orig = {}
go2children_empty = set()
for goobj in go2obj.values():
children = goobj.get_all_children()
if children:
go2children_orig[goobj.id] = children
else:
go2children_empty.add(goobj.id)
tic = prt_hms(tic,
"Get all goobj's children using GOTerm.get_all_children()",
prt)
# Get all children for all GO IDs using GOTerm get_all_children
go2children_fast = get_id2children(go2obj.values())
prt_hms(tic, "Get all goobj's children using go_tasks::get_id2children",
prt)
# Compare children lists
CheckGOs('test_get_children', go2obj).chk_a2bset(go2children_orig,
go2children_fast)
def test_get_lowerselect(prt=sys.stdout):
"""Test getting parents and user-specfied ancestor relationships"""
# Load GO-DAG
repo = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")
godag = get_godag(os.path.join(repo, 'go-basic.obo'), optional_attrs='relationship')
run = RelationshipCombos(godag)
run.chk_relationships_all()
rels_combo = run.get_relationship_combos()
print('{N} COMBINATIONS OF RELATIONSHIPS'.format(N=len(rels_combo)))
for relidx, rels_set in enumerate(rels_combo, 1):
print('{I}) RELATIONSHIPS[{N}]: {Rs}'.format(
I=relidx, N=len(rels_set), Rs=' '.join(sorted(rels_set))))
# ------------------------------------------------------------------------
# Get all parents for all GO IDs using get_all_parents in GOTerm class
tic = timeit.default_timer()
# pylint: disable=line-too-long
go2lowerselect_orig = {o.item_id:get_all_lowerselect(o, rels_set) for o in run.go2obj.values()}
tic = prt_hms(tic, "Get all goobj's parents using get_all_lowerselect(GOTerm)", prt)
# ------------------------------------------------------------------------
# Get all parents for all GO IDs using GOTerm get_all_parents
go2lowerselect_fast = get_id2lowerselect(run.go2obj.values(), rels_set)
tic = prt_hms(tic, "Get all goobj's parents using go_tasks::get_id2lowerselect", prt)
# ------------------------------------------------------------------------
# Compare parent lists
chkr = CheckGOs('test_get_lower_select', godag)
chkr.chk_a2bset(go2lowerselect_orig, go2lowerselect_fast) # EXPECTED, ACTUAL
print("PASSED: get_lowerselect RELATIONSHIPS[{N}]: {Rs}".format(
N=len(rels_set), Rs=' '.join(sorted(rels_set))))
def chk_get_goterms_upper(self):
"""Check that GOTerm's 'get_upper' returns parents and relationships."""
tic = timeit.default_timer()
for goterm in self.go2obj.values():
goids_act = set(o.item_id for o in goterm.get_goterms_upper())
goids_exp = self._get_goterms_upper(goterm.item_id)
assert goids_act == goids_exp
prt_hms(tic, "get_goterms_upper")
def chk_get_goterms_upper(self):
"""Check that GOTerm's 'get_upper' returns parents and relationships."""
tic = timeit.default_timer()
for goterm in self.go2obj.values():
goids_act = set(o.item_id for o in goterm.get_goterms_upper())
goids_exp = self._get_goterms_upper(goterm.item_id)
assert goids_act == goids_exp
prt_hms(tic, "get_goterms_upper")
def test_deprecatedloc_godagtimed():
"""Test deprecated location of GoDagTimed"""
tic = timeit.default_timer()
prt_hms(tic, 'prt_hms TESTED')
fin_go_obo = os.path.join(REPO, "go-basic.obo")
download_go_basic_obo(fin_go_obo, loading_bar=None)
GoDagTimed(fin_go_obo)
def chk_get_goterms_lower(self):
"""Check that GOTerm's 'get_lower' returns parents and relationships."""
tic = timeit.default_timer()
for goterm in self.go2obj.values():
goids_act = set(o.item_id for o in goterm.get_goterms_lower())
goids_exp = self._get_goterms_lower(goterm.item_id)
assert goids_act == goids_exp, "{GO} EXP({E}) ACT({A})".format(
GO=goterm.item_id, E=goids_exp, A=goids_act)
prt_hms(tic, "get_goterms_lower")
def chk_get_goterms_lower(self):
"""Check that GOTerm's 'get_lower' returns parents and relationships."""
tic = timeit.default_timer()
for goterm in self.go2obj.values():
goids_act = set(o.item_id for o in goterm.get_goterms_lower())
goids_exp = self._get_goterms_lower(goterm.item_id)
assert goids_act == goids_exp, "{GO} EXP({E}) ACT({A})".format(
GO=goterm.item_id, E=goids_exp, A=goids_act)
prt_hms(tic, "get_goterms_lower")
def get_gosubdag_r1(self, goids):
"""Return a GoSubDag with N randomly chosen GO sources."""
tic = timeit.default_timer()
gosubdag = GoSubDag(goids, self.godag_r1, relationships=True,
#rcntobj=self.gosubdag_r1.rcntobj,
prt=None)
prt_hms(tic, "GoSubDag r1 {N:4} GOs {S:3} srcs".format(
N=len(gosubdag.go2obj), S=len(gosubdag.go_sources)))
return gosubdag
def get_gosubdag_r0(self, goids):
"""Return a GoSubDag with N randomly chosen GO sources."""
tic = timeit.default_timer()
gosubdag = GoSubDag(
goids,
self.godag_r0,
relationships=None,
#rcntobj=self.gosubdag_r0.rcntobj,
prt=None)
prt_hms(
tic, "GoSubDag r0 {N:4} GOs {S:3} srcs".format(
N=len(gosubdag.go2obj), S=len(gosubdag.go_sources)))
return gosubdag
def __init__(self):
download_go_basic_obo(self.obo, sys.stdout, loading_bar=None)
self.godag_r0 = GODag(self.obo)
self.godag_r1 = GODag(self.obo, optional_attrs=set(['relationship']))
self.goids = list(set(o.id for o in self.godag_r0.values()))
# GoSubDag (plain)
tic = timeit.default_timer()
self.gosubdag_r0 = GoSubDag(self.goids, self.godag_r0, prt=None)
prt_hms(tic, "GoSubDag r0 {N:4} GOs {S:3} srcs".format(
N=len(self.gosubdag_r0.go2obj), S=len(self.gosubdag_r0.go_sources)))
# GoSubDag with relationships
self.gosubdag_r1 = GoSubDag(self.goids, self.godag_r1, prt=None, relationships=True)
prt_hms(tic, "GoSubDag r1 {N:4} GOs {S:3} srcs".format(
N=len(self.gosubdag_r1.go2obj), S=len(self.gosubdag_r1.go_sources)))
def test_update_association():
"""Compare new propagate cnts function with original function. Test assc results is same."""
print('\n1) READ GODAG:')
assc_name = "goa_human.gaf" # gene_association.fb gene_association.mgi
obo = os.path.join(REPO, "go-basic.obo")
tic = timeit.default_timer()
godag = get_godag(obo)
tic = prt_hms(tic, "Created two GODags: One for original and one for new propagate counts")
print('\n2) READ ANNOTATIONS:')
assc_orig = dnld_assc(os.path.join(REPO, assc_name), godag)
tic = prt_hms(tic, "Associations Read")
objanno = get_objanno(os.path.join(REPO, assc_name), 'gaf', godag=godag)
tic = prt_hms(tic, "Associations Read")
print('\n3) MAKE COPIES OF ASSOCIATIONS:')
assc1 = {g:set(gos) for g, gos in assc_orig.items()}
assc2 = {g:set(gos) for g, gos in assc_orig.items()}
tic = prt_hms(tic, "Associations Copied: One for original and one for new")
print('\n4) UPDATE ASSOCIATIONS (PROPAGATE COUNTS):')
godag.update_association(assc1)
tic = prt_hms(tic, "ORIG: godag.update_association(assc)")
update_association(assc2, godag)
tic = prt_hms(tic, "NEW SA: update_association(go2obj, assc_orig)")
assc3 = objanno.get_id2gos(namespace='BP', propagate_counts=True)
tic = prt_hms(tic, "NEW BASE: update_association(go2obj, assc_orig)")
print('\n5) RUN CHECKS')
_chk_assc(assc1, assc2)
_chk_assc(assc1, assc3)
_chk_godag(godag, obo)
def test_get_children(prt=sys.stdout):
"""Semantic Similarity test for Issue #86."""
# Load GO-DAG
fin_obo = "go-basic.obo"
repo = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")
godag = get_godag(os.path.join(repo, fin_obo))
go2obj = {go:o for go, o in godag.items() if go == o.id}
# Get all children for all GO IDs using get_all_children in GOTerm class
tic = timeit.default_timer()
go2children_orig = {}
for goobj in go2obj.values():
go2children_orig[goobj.id] = goobj.get_all_children()
tic = prt_hms(tic, "Get all goobj's children using GOTerm.get_all_children()", prt)
# Get all children for all GO IDs using GOTerm get_all_children
go2children_fast = get_id2children(go2obj.values())
prt_hms(tic, "Get all goobj's children using go_tasks::get_go3children", prt)
# Compare children lists
_chk_a2bset(go2children_orig, go2children_fast)
def test_get_parent(prt=sys.stdout):
"""Semantic Similarity test for Issue #86."""
# Load GO-DAG
fin_obo = "go-basic.obo"
repo = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")
godag = get_godag(os.path.join(repo, fin_obo))
go2obj = {go: o for go, o in godag.items() if go == o.id}
# Get all parents for all GO IDs using get_all_parents in GOTerm class
tic = timeit.default_timer()
go2parents_orig = {}
for goobj in go2obj.values():
go2parents_orig[goobj.id] = goobj.get_all_parents()
tic = prt_hms(tic,
"Get all goobj's parents using GOTerm.get_all_parents()",
prt)
# Get all parents for all GO IDs using GOTerm get_all_parents
go2parents_fast = get_go2parents(go2obj.values())
prt_hms(tic, "Get all goobj's parents using go_tasks::get_go2parents", prt)
# Compare parent lists
_chk_a2bset(go2parents_orig, go2parents_fast)
print("PASSED: get_parent test")
def __init__(self):
download_go_basic_obo(self.obo, sys.stdout, loading_bar=None)
self.godag_r0 = GODag(self.obo)
self.godag_r1 = GODag(self.obo, optional_attrs=set(['relationship']))
self.goids = list(set(o.id for o in self.godag_r0.values()))
# GoSubDag (plain)
tic = timeit.default_timer()
self.gosubdag_r0 = GoSubDag(self.goids, self.godag_r0, prt=None)
prt_hms(
tic, "GoSubDag r0 {N:4} GOs {S:3} srcs".format(
N=len(self.gosubdag_r0.go2obj),
S=len(self.gosubdag_r0.go_sources)))
# GoSubDag with relationships
self.gosubdag_r1 = GoSubDag(self.goids,
self.godag_r1,
prt=None,
relationships=True)
prt_hms(
tic, "GoSubDag r1 {N:4} GOs {S:3} srcs".format(
N=len(self.gosubdag_r1.go2obj),
S=len(self.gosubdag_r1.go_sources)))
def test_get_parent(prt=sys.stdout):
"""Semantic Similarity test for Issue #86."""
# Load GO-DAG
fin_obo = "go-basic.obo"
repo = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")
godag = get_godag(os.path.join(repo, fin_obo))
go2obj = {go: o for go, o in godag.items() if go == o.id}
# ------------------------------------------------------------------------
# Get all parents for all GO IDs using get_all_parents in GOTerm class
tic = timeit.default_timer()
go2parents_orig = {}
## go_noparents = set()
for goterm in go2obj.values():
parents = goterm.get_all_parents()
#if parents:
go2parents_orig[goterm.id] = parents
#else:
# go_noparents.add(goterm.id)
tic = prt_hms(tic,
"Get all goobj's parents using GOTerm.get_all_parents()",
prt)
# ------------------------------------------------------------------------
# Get all parents for all GO IDs using GOTerm get_all_parents
go2parents_fast = get_id2parents(go2obj.values())
tic = prt_hms(tic,
"Get all goobj's parents using go_tasks::get_id2parents",
prt)
# ------------------------------------------------------------------------
go2parents_fast2 = get_id2parents2(go2obj.values())
tic = prt_hms(tic,
"Get all goobj's parents using go_tasks::get_id2parents2",
prt)
# ------------------------------------------------------------------------
# Compare parent lists
chkr = CheckGOs('test_get_parents', go2obj)
chkr.chk_a2bset_equiv(go2parents_orig, go2parents_fast)
chkr.chk_a2bset_equiv(go2parents_orig, go2parents_fast2)
print("PASSED: get_parent test")
