def test_iter(self):
assoc = InSqlAssoc(GAF20FIELDS, [1, 4], lambda x: x)
with open('Ontology/GoaIO/no_ver.fb', 'r') as f:
for r in TsvIterator(f):
if len(r) == 17:
assoc.add_row(r)
self.assertEqual(
[(u'FBgn0026619',
[(u'FB', u'FBgn0026615', u'10-4', u'', u'GO:0005737',
u'FB:FBrf0106275', u'IDA', u'', u'C', u'10-4', u'',
u'gene_product', u'taxon:7227', u'20060803', u'FlyBase', u'',
u''),
(u'FB', u'FBgn0026615', u'10-4', u'', u'GO:0045177',
u'FB:FBrf0106275', u'IDA', u'', u'C', u'10-4', u'',
u'gene_product', u'taxon:7227', u'20060803', u'FlyBase', u'',
u'')]),
(u'FBgn0043467', [
(u'FB', u'FBgn0026619', u'10-4', u'', u'GO:0045177',
u'FB:FBrf0106275', u'IDA', u'', u'C', u'10-4', u'',
u'gene_product', u'taxon:7227', u'20060803', u'FlyBase', u'',
u'')
]),
(u'FBgn0043467', [
(u'FB', u'FBgn0043467', u'064Ya', u'', u'GO:0048149',
u'FB:FBrf0131396|PMID:11086999', u'IMP', u'', u'P', u'064Ya',
u'', u'gene_product', u'taxon:7227', u'20060803', u'FlyBase',
u'', u''),
(u'FB', u'FBgn0043467', u'064Ya', u'', u'GO:0005575',
u'FB:FBrf0159398', u'ND', u'', u'C', u'064Ya', u'',
u'gene_product', u'taxon:7227', u'20060803', u'FlyBase', u'',
u'')
])], list(assoc))
def test_insert_get_len(self):
assoc = InSqlAssoc(GAF20FIELDS, [1, 4], lambda x: x)
self.assertEquals(0, len(assoc))
with open("Ontology/GoaIO/no_ver.fb", "r") as f:
for r in TsvIterator(f):
if len(r) == 17:
assoc.add_row(r)
self.assertEquals(3, len(assoc))
self.assertEquals(
[
(
u"FB",
u"FBgn0043467",
u"064Ya",
u"",
u"GO:0005575",
u"FB:FBrf0159398",
u"ND",
u"",
u"C",
u"064Ya",
u"",
u"gene_product",
u"taxon:7227",
u"20060803",
u"FlyBase",
u"",
u"",
),
(
u"FB",
u"FBgn0043467",
u"064Ya",
u"",
u"GO:0048149",
u"FB:FBrf0131396|PMID:11086999",
u"IMP",
u"",
u"P",
u"064Ya",
u"",
u"gene_product",
u"taxon:7227",
u"20060803",
u"FlyBase",
u"",
u"",
),
],
sorted(assoc["FBgn0043467"]),
)
self.assertTrue("FBgn0043467" in assoc)
def test_insert_get_len(self):
assoc = InSqlAssoc(GAF20FIELDS, [1, 4], lambda x: x)
self.assertEquals(0, len(assoc))
with open('Ontology/GoaIO/no_ver.fb', 'r') as f:
for r in TsvIterator(f):
if len(r) == 17:
assoc.add_row(r)
self.assertEquals(3, len(assoc))
self.assertEquals([
(u'FB', u'FBgn0043467', u'064Ya', u'', u'GO:0005575',
u'FB:FBrf0159398', u'ND', u'', u'C', u'064Ya', u'',
u'gene_product', u'taxon:7227', u'20060803', u'FlyBase', u'',
u''),
(u'FB', u'FBgn0043467', u'064Ya', u'', u'GO:0048149',
u'FB:FBrf0131396|PMID:11086999', u'IMP', u'', u'P', u'064Ya', u'',
u'gene_product', u'taxon:7227', u'20060803', u'FlyBase', u'', u'')
], sorted(assoc['FBgn0043467']))
self.assertTrue('FBgn0043467' in assoc)
def test_iter(self):
assoc = InSqlAssoc(GAF20FIELDS, [1, 4], lambda x: x)
with open("Ontology/GoaIO/no_ver.fb", "r") as f:
for r in TsvIterator(f):
if len(r) == 17:
assoc.add_row(r)
self.assertEqual(
[
(
u"FBgn0026619",
[
(
u"FB",
u"FBgn0026615",
u"10-4",
u"",
u"GO:0005737",
u"FB:FBrf0106275",
u"IDA",
u"",
u"C",
u"10-4",
u"",
u"gene_product",
u"taxon:7227",
u"20060803",
u"FlyBase",
u"",
u"",
),
(
u"FB",
u"FBgn0026615",
u"10-4",
u"",
u"GO:0045177",
u"FB:FBrf0106275",
u"IDA",
u"",
u"C",
u"10-4",
u"",
u"gene_product",
u"taxon:7227",
u"20060803",
u"FlyBase",
u"",
u"",
),
],
),
(
u"FBgn0043467",
[
(
u"FB",
u"FBgn0026619",
u"10-4",
u"",
u"GO:0045177",
u"FB:FBrf0106275",
u"IDA",
u"",
u"C",
u"10-4",
u"",
u"gene_product",
u"taxon:7227",
u"20060803",
u"FlyBase",
u"",
u"",
)
],
),
(
u"FBgn0043467",
[
(
u"FB",
u"FBgn0043467",
u"064Ya",
u"",
u"GO:0048149",
u"FB:FBrf0131396|PMID:11086999",
u"IMP",
u"",
u"P",
u"064Ya",
u"",
u"gene_product",
u"taxon:7227",
u"20060803",
u"FlyBase",
u"",
u"",
),
(
u"FB",
u"FBgn0043467",
u"064Ya",
u"",
u"GO:0005575",
u"FB:FBrf0159398",
u"ND",
u"",
u"C",
u"064Ya",
u"",
u"gene_product",
u"taxon:7227",
u"20060803",
u"FlyBase",
u"",
u"",
),
],
),
],
list(assoc),
)