Example #1
0
 def test_cache(self):
     np.random.seed(0)
     aligner, query, exp_fp = self.blast
     pred = FeatureAnnt([self.db], mkdtemp(dir=self.tmp_dir),
                        cache=self.cache)
     obs = pred(query, aligner=aligner)
     exp = pred.parse_tabular(exp_fp)
     self.assertEquals(exp['sseqid'].values, obs['sseqid'].values)
Example #2
0
 def test_cache_empty_db(self):
     np.random.seed(0)
     for test in self.tests:
         aligner, query, exp_fp = test.aligner, test.input, test.exp
         pred = FeatureAnnt([], mkdtemp(dir=self.tmp_dir), cache=self.cache)
         obs = pred(query, aligner=aligner)
         exp = pred._filter_best(pred.parse_tabular(exp_fp))
         self.assertEqual(exp['sseqid'].values, obs['sseqid'].values)
Example #3
0
 def test_cache_empty_db(self):
     np.random.seed(0)
     for test in self.tests:
         aligner, query, exp_fp = test.aligner, test.input, test.exp
         pred = FeatureAnnt([], mkdtemp(dir=self.tmp_dir),
                            cache=self.cache)
         obs = pred(query, aligner=aligner)
         exp = pred._filter_best(pred.parse_tabular(exp_fp))
         self.assertEqual(exp['sseqid'].values, obs['sseqid'].values)
Example #4
0
 def test_blast(self):
     for test in self.tests:
         pred = FeatureAnnt([self.db], mkdtemp(dir=self.tmp_dir))
         obs = pred(test.input, aligner=test.aligner, outfmt='tab')
         exp = pred._filter_best(
             pred.parse_tabular('%s.diamond' % test.exp))
         self.assertTrue(exp.equals(obs))
         obs = pred(test.input, aligner=test.aligner, outfmt='sam')
         exp = pred._filter_id_cov(pred.parse_sam('%s.sam' % test.exp))
         self.assertTrue(exp.equals(obs))
Example #5
0
    def test_parse_sam_best(self):
        for test in self.blast:
            df = FeatureAnnt.parse_sam(test[2], column='bitscore')
            df = df.reindex_axis(sorted(df.columns), axis=1)
            exp = df.reindex_axis(sorted(self.exp.columns), axis=1)

            pdt.assert_frame_equal(df, exp)
Example #6
0
 def test_blast_wrong_input(self):
     pred = FeatureAnnt([self.db], self.tmp_dir)
     for i in self.neg_fp:
         for aligner in ['blastp', 'blastx']:
             with self.assertRaisesRegex(
                     ApplicationError,
                     r'(Error reading file)|(Invalid input file format)'):
                 pred(i, aligner=aligner)
Example #7
0
 def test_cache_initialize(self):
     np.random.seed(0)
     for test in self.tests:
         aligner, query = test.aligner, test.input
         pred = FeatureAnnt([self.db],
                            mkdtemp(dir=self.tmp_dir),
                            cache=DiamondCache())
         pred(query, aligner=aligner)
         self.assertTrue(len(pred.cache.seqs) > 0)
Example #8
0
 def test_blast(self):
     for test in self.tests:
         pred = FeatureAnnt([self.db], mkdtemp(dir=self.tmp_dir))
         obs = pred(test.input, aligner=test.aligner, outfmt='tab')
         exp = pred._filter_best(pred.parse_tabular('%s.diamond' %
                                                    test.exp))
         self.assertTrue(exp.equals(obs))
         obs = pred(test.input, aligner=test.aligner, outfmt='sam')
         exp = pred._filter_id_cov(pred.parse_sam('%s.sam' % test.exp))
         self.assertTrue(exp.equals(obs))
Example #9
0
 def test_filter_id_cov(self):
     for test in self.filter_tests2:
         df = FeatureAnnt.parse_sam(test.input)
         df_filter = FeatureAnnt._filter_id_cov(df, pident=30, cov=92)
         df_filter.to_csv(test.obs, sep='\t')
         self.assertTrue(cmp(test.exp, test.obs, shallow=False))
Example #10
0
 def test_filter_best(self):
     for test in self.filter_tests:
         df = FeatureAnnt.parse_tabular(test.input)
         df_filter = FeatureAnnt._filter_best(df)
         df_filter.to_csv(test.obs, sep='\t')
         self.assertTrue(cmp(test.exp, test.obs, shallow=False))
Example #11
0
 def test_parse_sam(self):
     for test in self.sam_tests:
         df = FeatureAnnt.parse_sam(test.input)
         df.to_csv(test.obs, sep='\t', index=False)
         self.assertTrue(cmp(test.exp, test.obs, shallow=False))
Example #12
0
 def test_blast(self):
     for aligner, query, exp_fp in self.blast:
         pred = FeatureAnnt([self.db], mkdtemp(dir=self.tmp_dir))
         obs = pred(query, aligner=aligner)
         exp = pred.parse_tabular(exp_fp)
         self.assertTrue(exp.equals(obs))
Example #13
0
 def test_filter_id_cov(self):
     for test in self.filter_tests2:
         df = FeatureAnnt.parse_sam(test.input)
         df_filter = FeatureAnnt._filter_id_cov(df, pident=30, cov=92)
         df_filter.to_csv(test.obs, sep='\t')
         self.assertTrue(cmp(test.exp, test.obs, shallow=False))
Example #14
0
 def test_filter_best(self):
     for test in self.filter_tests:
         df = FeatureAnnt.parse_tabular(test.input)
         df_filter = FeatureAnnt._filter_best(df)
         df_filter.to_csv(test.obs, sep='\t')
         self.assertTrue(cmp(test.exp, test.obs, shallow=False))
Example #15
0
 def test_parse_sam(self):
     for test in self.sam_tests:
         df = FeatureAnnt.parse_sam(test.input)
         df.to_csv(test.obs, sep='\t', index=False)
         self.assertTrue(cmp(test.exp, test.obs, shallow=False))
Example #16
0
 def test_blast(self):
     for test in self.tests:
         pred = FeatureAnnt([self.db], mkdtemp(dir=self.tmp_dir))
         obs = pred(test.input, aligner=test.aligner)
         exp = pred._filter_best(pred.parse_tabular(test.exp))
         self.assertTrue(exp.equals(obs))