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)
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)
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)
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))
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)
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)
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)
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))
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))
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))
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))
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))
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))
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))
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))
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))