def test_obsolete_replair_of_withfrom():
p = GafParser(config=assocparser.AssocParserConfig(
ontology=OntologyFactory().create(OBSOLETE_ONT)))
assocs = p.parse(open(ZFIN_GAF, "r"), skipheader=True)
assert assocs[0].evidence.with_support_from == [
ConjunctiveSet(elements=[Curie(namespace='GO', identity='0005912')])
]
# Reset parser report
p = GafParser(config=assocparser.AssocParserConfig(
ontology=OntologyFactory().create(OBSOLETE_ONT)))
p.version = "2.2"
obsolete_no_replacement_line = "FB\tFBgn0003334\tScm\tlocated_in\tGO:0005634\tFB:FBrf0179383|PMID:15280237\tIC\tGO:0016458\tC\tSex comb on midleg\tCG9495|SCM|Sex Comb on Midleg|Sex Comb on the Midleg|Sex combs on midleg|Sex combs on midlegs|Su(z)302|l(3)85Ef|scm|sex comb on midleg\tprotein\ttaxon:7227\t20050203\tUniProt\t\t"
assoc_result = p.parse_line(obsolete_no_replacement_line)
assert assoc_result.associations == []
assert p.report.to_report_json(
)["messages"]["gorule-0000020"][0]["obj"] == "GO:0016458"
def test_validate_go_idspaces():
ont = OntologyFactory().create(ONT)
p = GafParser()
p.config.class_idspaces = ['FOOZ']
assocs = p.parse(open(POMBASE, "r"))
for m in p.report.messages:
print("MESSAGE: {}".format(m))
assert len(assocs) == 0
assert len(p.report.messages) > 1
summary = p.report.to_report_json()['summary']
assert summary['association_count'] == 0
assert summary['line_count'] > 300
print(p.report.to_markdown())
# ensure config is not preserved
p = GafParser()
assert p.config.class_idspaces == None
def test_qualifiers_gaf_2_2():
p = GafParser()
assocs = p.parse(open("tests/resources/test-qualifiers-2.2.gaf"),
skipheader=True)
# NOT by itself is not allowed
assert len(
list(
filter(
lambda e: e["obj"] == "NOT",
p.report.to_report_json()["messages"]["gorule-0000001"]))) == 1
assert len(
list(
filter(
lambda e: e["obj"] == "contributes_to|enables",
p.report.to_report_json()["messages"]["gorule-0000001"]))) == 1
assert len([
a for a in assocs
if association.Curie.from_str("RO:0004035") in a.qualifiers
]) == 1
def test_qualifiers_gaf():
p = GafParser()
assocs = p.parse(open(QGAF, "r"), skipheader=True)
neg_assocs = [a for a in assocs if a.negated == True]
assert len(neg_assocs) == 3
for a in assocs:
print('REL: {}'.format(str(a.relation)))
assert len([a for a in assocs if str(a.relation) == 'RO:0002326']) == 1
# For the space in `colocalizes with`
assert len(
list(
filter(
lambda e: e["obj"] == "colocalizes with",
p.report.to_report_json()["messages"]["gorule-0000001"]))) == 1
assert len(
list(
filter(
lambda e: e["obj"] == "involved_in",
p.report.to_report_json()["messages"]["gorule-0000001"]))) == 1
def test_qualifiers_gaf_2_2():
p = GafParser()
assocs = p.parse(open("tests/resources/test-qualifiers-2.2.gaf"),
skipheader=True)
# NOT by itself is not allowed
assert len(
list(
filter(
lambda e: e["obj"] == "NOT",
p.report.to_report_json()["messages"]["gorule-0000001"]))) == 1
assert len(
list(
filter(
lambda e: e["obj"] == "contributes_to|enables",
p.report.to_report_json()["messages"]["gorule-0000001"]))) == 1
assert len([
a for a in assocs
if "acts_upstream_of_negative_effect" in a["qualifiers"]
]) == 1
def test_errors_gaf():
p = GafParser()
p.config.ecomap = EcoMap()
assocs = p.parse(open("tests/resources/errors.gaf", "r"))
msgs = p.report.messages
print("MESSAGES: {}".format(len(msgs)))
for m in msgs:
print("MESSAGE: {}".format(m))
assert len(msgs) == 15
# we expect 4
assert len(assocs) == 7
from ontobio.io import GafWriter
w = GafWriter()
w.write(assocs)
xs = [x for a in assocs for x in a.get('object_extensions', [])]
for x in xs:
print('X: {}'.format(x))
# ensure that invalid expressions have been eliminated
assert x['property'] == 'foo'
assert x['filler'] == 'X:1'
assert len(xs) == 3
def parse(self, limit=None):
"""
Override Source.parse()
Args:
:param limit (int, optional) limit the number of rows processed
Returns:
:return None
"""
if limit is not None:
LOG.info("Only parsing first %d rows", limit)
rgd_file = '/'.join(
(self.rawdir, self.files['rat_gene2mammalian_phenotype']['file']))
# ontobio gafparser implemented here
p = GafParser()
assocs = p.parse(open(rgd_file, "r"))
for i, assoc in enumerate(assocs):
if 'relation' in assoc.keys():
self.make_association(assoc)
if limit is not None and i > limit:
break
return
def parse(self, limit=None):
"""
Override Source.parse()
Args:
:param limit (int, optional) limit the number of rows processed
Returns:
:return None
"""
if limit is not None:
LOG.info("Only parsing first %d rows", limit)
rgd_file = '/'.join(
(self.rawdir, self.files['rat_gene2mammalian_phenotype']['file']))
# ontobio gafparser implemented here
p = GafParser()
assocs = p.parse(open(rgd_file, "r"))
for i, assoc in enumerate(assocs):
if 'relation' in assoc.keys():
self.make_association(assoc)
if limit is not None and i > limit:
break
return
def test_map2slim_gaf():
f = POMBASE
p = GafParser()
is_gaf = f == POMBASE
ont = OntologyFactory().create(ONT)
relations=['subClassOf', 'BFO:0000050']
# creates a basic JSON dictionary
m = ont.create_slim_mapping(subset_nodes=SUBSET, relations=relations)
assert m['GO:0071423'] == ['GO:0006810']
assert len(m[NESRA]) == 2
assert 'GO:0051169' in m[NESRA]
assert 'GO:0003674' in m[NESRA]
outfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
p.map_to_subset(open(f,"r"), class_map=m, outfile=outfile)
for m in p.report.messages:
logging.debug("MESSAGE1: {}".format(m))
for m in p.report.messages:
logging.debug("MESSAGE1: {}".format(m))
logging.info("MESSAGES: {}".format(len(p.report.messages)))
p = GafParser()
logging.info("CLOSING: {}".format(outfile))
outfile.close()
logging.info("Reading from: {}".format(outfile.name))
assocs = p.parse(outfile.name)
for m in p.report.messages:
logging.debug("MESSAGE2: {}".format(m))
assert len(assocs) > 100
cls_ids = set()
for a in assocs:
cid = a['object']['id']
assert cid in SUBSET
cls_ids.add(cid)
print(str(a))
print(cls_ids)
def test_parse():
ont = OntologyFactory().create(ONT)
p = GafParser()
assocs = p.parse(open(POMBASE, "r"))
#gen(assocs,SimpleAssocRdfTransform(),'simple')
gen(assocs, CamRdfTransform(), 'cam')
def test_default_gaf_version():
p = GafParser()
assocs = p.parse(open("tests/resources/test-qualifiers-no-version.gaf"), skipheader=True)
assert p.version == "2.1"
