Exemplo n.º 1
0
    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))
Exemplo n.º 2
0
    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)
Exemplo n.º 3
0
    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)
Exemplo n.º 4
0
    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),
        )