def setUp(self):
self.go = OBO('files/test_data/go.obo')
self.go.populate_annotations(GO_URL, remote_location=True)
self.dsrepair_term = self.go.get_term(DSREPAIR_ID)
lines = open('files/go_neg_slim.txt').readlines()
self.slim_terms = set([l.strip() for l in lines])
class TestLabels(unittest.TestCase):
def setUp(self):
self.go = OBO('files/test_data/go.obo')
self.go.populate_annotations(GO_URL, remote_location=True)
self.dsrepair_term = self.go.get_term(DSREPAIR_ID)
lines = open('files/go_neg_slim.txt').readlines()
self.slim_terms = set([l.strip() for l in lines])
def testOntoLabelsNeg(self):
ol = OntoLabels(obo=self.go, slim_terms=self.slim_terms)
(pos, neg) = ol.get_labels(DSREPAIR_ID)
self.assertTrue(len(pos) > 0)
self.assertEqual(pos,set(self.dsrepair_term.get_annotated_genes()))
similar_term = self.go.get_term(DNA_REP_ID).get_annotated_genes()
slim_overlap = self.go.get_ancestors(DNA_REP_ID) & \
self.go.get_ancestors(DSREPAIR_ID) & \
self.slim_terms
self.assertTrue(DNA_METAB in slim_overlap)
self.assertTrue(len(neg & set(similar_term)) == 0)
for dterm in self.go.get_descendents(DNA_METAB):
dgenes = set(self.go.get_term(dterm).get_annotated_genes())
self.assertTrue(len(neg & dgenes) == 0)
class TestOBO(unittest.TestCase):
def setUp(self):
self.go = OBO('files/test_data/go.obo')
self.dsrepair_term = self.go.get_term(DSREPAIR_ID)
def test_load_remote(self):
"""Test loading an obo file from a URL"""
self.go = OBO()
self.go.load_obo(GO_URL, remote_location=True)
self.test_load()
def test_load(self):
"""Test an obo is loaded"""
# Check that root biologcal process term is loaded
term = self.go.get_term('GO:0008150')
self.assertTrue(term is not None and term.name == 'biological_process')
self.assertTrue(len(term.parent_of) > 0)
def test_add_annotation(self):
"""Test that adding a gene annotations is correct"""
self.assertTrue(self.dsrepair_term is not None)
self.dsrepair_term.add_annotation('672')
genes = self.dsrepair_term.get_annotated_genes()
self.assertEqual(genes[0], '672')
def test_propagation(self):
"""Test that gene propagation adds annotations to the correct terms"""
self.assertTrue(self.dsrepair_term is not None)
self.dsrepair_term.add_annotation('672')
self.go.propagate()
term_count = 0
for term in self.go.get_termobject_list():
term_count += len(term.get_annotated_genes())
self.assertEqual(term_count, 26)
def test_direct_annotation(self):
"""Test that direct annotation status is preserved"""
self.assertTrue(self.dsrepair_term is not None)
self.go.add_annotation(go_id=DSREPAIR_ID,
gid='672',
ref=None,
direct=True)
self.go.propagate()
direct_count, total = 0, 0
for term in self.go.get_termobject_list():
for a in term.annotations:
if a.direct:
direct_count += 1
self.assertEqual(term, self.dsrepair_term)
total += 1
self.assertEqual(direct_count, 1)
self.assertEqual(total, 26)
def test_ancestors(self):
"""Test that ancestor terms are correct"""
self.assertTrue(self.dsrepair_term is not None)
self.assertEqual(len(self.go.get_ancestors(self.dsrepair_term.go_id)),
25)
def test_parents(self):
"""Test that parent terms are stored correctly"""
parents = self.dsrepair_term.child_of
self.assertEqual(len(parents), 2)
self.assertTrue(GOTerm('GO:0006302') in parents)
self.assertTrue(GOTerm('GO:0000725') in parents)
def test_heads(self):
"""Test that there are only three head nodes, corresponding to:
biological process, molecular function, and cellular component
"""
heads = set(
[term for term in self.go.get_termobject_list() if term.head])
self.assertEqual(len(heads), 3)
self.assertTrue(GOTerm('GO:0008150') in heads)
self.assertTrue(GOTerm('GO:0003674') in heads)
self.assertTrue(GOTerm('GO:0005575') in heads)
def test_obsolete(self):
"""Test that none of the stored terms are obsolete"""
for term in self.go.get_termobject_list():
self.assertTrue(not term.obsolete)
for term in self.go.get_obsolete_terms():
self.assertTrue(term.obsolete)
def test_term_equals(self):
"""Test GOTerm equals method"""
self.assertEqual(self.dsrepair_term, GOTerm(DSREPAIR_ID))
def tearDown(self):
self.go = None
self.dsrepair_term = None
def test_load_remote(self):
"""Test loading an obo file from a URL"""
self.go = OBO()
self.go.load_obo(GO_URL, remote_location=True)
self.test_load()
def setUp(self):
self.go = OBO('files/test_data/go.obo')
self.dsrepair_term = self.go.get_term(DSREPAIR_ID)
args = parser.parse_args()
if args.obo is None:
sys.stderr.write("--obo file is required.\n")
sys.exit()
if args.pub_filter and args.nspace is None:
sys.stderr.write(
"--When filtering by publication, must provide GO namespace.\n")
sys.exit()
id_name = None
if args.idfile is not None:
id_name = IDMap(args.idfile)
gene_ontology = OBO(args.obo)
logger.info('Populating gene associations')
if args.ass:
gene_ontology.populate_annotations(args.ass,
gene_col=args.gcol,
term_col=args.term_col)
elif args.gmt:
gmt = GMT(args.gmt)
gene_ontology.populate_annotations_from_gmt(gmt)
else:
sys.stderr.write(
"--Provide gene annotations from an association file or a GMT file")
exit()
if args.pub_filter:
help='List of background genes')
args = parser.parse_args()
ubiq = None
if args.ubiq_genes:
ubiq = set()
with open(args.ubiq_genes) as f:
for l in f.readlines():
ubiq.add(l.strip())
logger.info('Total ubiquitous genes: %i', len(ubiq))
onto = None
if args.tissue_onto:
onto = OBO(args.tissue_onto)
tissue_genes = GMT(args.tissue_genes)
if onto:
onto.populate_annotations_from_gmt(tissue_genes)
onto.propagate()
tissue_genes = onto.as_gmt()
with open(args.pos) as f:
edge_lines = f.readlines()
tissue_std_edges = defaultdict(dict)
for line in edge_lines:
g1, g2, std = line.strip().split()[:3]