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_upperselect(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
go2upperselect_orig = {o.item_id:get_all_upperselect(o, rels_set) for o in run.go2obj.values()}
tic = prt_hms(tic, "Get all goobj's parents using get_all_upperselect(GOTerm)", prt)
# ------------------------------------------------------------------------
# Get all parents for all GO IDs using GOTerm get_all_parents
go2upperselect_fast = get_id2upperselect(run.go2obj.values(), rels_set)
tic = prt_hms(tic, "Get all goobj's parents using go_tasks::get_id2upperselect", prt)
# ------------------------------------------------------------------------
# Compare parent lists
chkr = CheckGOs('test_get_upper_select', godag)
chkr.chk_a2bset(go2upperselect_orig, go2upperselect_fast) # EXPECTED, ACTUAL
print("PASSED: get_upperselect RELATIONSHIPS[{N}]: {Rs}".format(
N=len(rels_set), Rs=' '.join(sorted(rels_set))))
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_pfenning".format(REPO=repo)
ntobj = cx.namedtuple("david6p8", "TOTAL FDR Bonferroni Benjamini PValue")
# pylint: disable=bad-whitespace
fin2exp = {
"david_chart6p8_Consistent_Decrease.txt":
ntobj._make([1773, 259, 249, 432, 1316]),
"david_chart6p8_Transient_Decrease.txt":
ntobj._make([423, 0, 2, 2, 246]),
"david_chart6p8_Consistent_Increase.txt":
ntobj._make([2359, 353, 308, 781, 1868]),
"david_chart6p8_Transient_Increase.txt":
ntobj._make([2191, 658, 652, 1105, 1786]),
"david_chart6p8_Late_Decrease.txt":
ntobj._make([2752, 591, 568, 1153, 2187]),
"david_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 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_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_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 _randoms(self, prt):
"""Randomly select GO terms for semantic similarity calculations"""
#pylint: disable=line-too-long
goids = self.goids
go_pairs = [(goids[i], goids[i + 1])
for i in range(0, len(self.goids), 2)]
tic = timeit.default_timer()
# Information on Python's round, which is used in 2 spots in pygosemsim:
# https://stackoverflow.com/questions/13479163/round-float-to-x-decimals
# from decimal import Decimal
# >>> Decimal('66.66666666666').quantize(Decimal('1e-4'))
# Decimal('66.6667')
# >>> Decimal('1.29578293').quantize(Decimal('1e-6'))
# Decimal('1.295783')
# In issue, https://github.com/micropython/micropython/issues/3516,
# https://github.com/mdickinson dreams of deprecating the two-argument form of round in Python....
# https://github.com/micropython/micropython/issues/3516#issuecomment-625298591
# Use the decimal type instead: https://docs.python.org/3.10/library/decimal.html
acts = [self.wang.get_sim(a, b) for a, b in go_pairs]
tic = prt_hms(tic, 'GOATOOLS wang calc')
exps = [similarity.wang(self.graph, a, b) for a, b in go_pairs]
tic = prt_hms(tic, 'pysemsim wang')
assert len(acts) == len(exps)
failures = 0
for idx, (act, exp, (go_a,
go_b)) in enumerate(zip(acts, exps, go_pairs)):
assert act is not None, self._prt_ab(idx, go_a, go_b, act, exp,
stdout)
assert exp is not None, self._prt_ab(idx, go_a, go_b, act, exp,
stdout)
if abs(exp - act) > 0.02:
for strm in [prt, stdout]:
go_a = goids[2 * idx]
go_b = goids[2 * idx + 1]
self._prt_ab(idx, go_a, go_b, act, exp, strm)
stdout.flush()
prt.flush()
failures += 1
self.prt_ancestors(go_a, True)
self.prt_ancestors(go_b, True)
else:
prt.write('{i} PASS {A} {B} pygosemsim={b:f} GOATOOLS={a:f}\n'.
format(i=idx,
A=goids[2 * idx],
B=goids[2 * idx + 1],
a=act,
b=exp))
def __init__(self, fin_godag, num_calcs, relationships, w_e, seed, prt):
tic = timeit.default_timer()
self.godag = get_godag(fin_godag,
optional_attrs=['relationship'],
prt=prt)
tic = prt_hms(tic, 'GOATOOLS read godag')
# Needed because pysemsim not understand cygwin pathes
self.graph = graph.from_resource(splitext(fin_godag)[0])
tic = prt_hms(tic, 'pygosemsim read godag')
self.seedobj = RandomSeed32(seed)
self.goids = self._init_goids(num_calcs)
tic = timeit.default_timer()
self.wang = SsWang(self.goids, self.godag, relationships, w_e)
self.go2reldepth = get_go2reldepth(
{self.godag[go]
for go in self.godag}, relationships)
tic = prt_hms(tic, 'GOATOOLS wang setup')
def test_i154_semsim_lin():
"""Test for issue 148, Lin Similarity if a term has no annotations"""
fin_dag = download_go_basic_obo()
tic = timeit.default_timer()
optional_attrs = {'consider', 'replaced_by'}
load_obsolete = True
prt = sys.stdout
godag = GODag(fin_dag, optional_attrs, load_obsolete, prt)
prt_hms(tic, 'Loaded GO DAG')
assert godag['GO:0000067'].consider
assert godag['GO:0003734'].replaced_by == 'GO:0030532'
godag = GODag(fin_dag, 'consider', load_obsolete, prt)
prt_hms(tic, 'Loaded GO DAG')
assert godag['GO:0000067'].consider
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 = 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(join(REPO, assc_name), godag, prt=stdout)
tic = prt_hms(tic, "Associations Read")
objanno = get_objanno(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 __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")