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_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_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))
