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)