def test_parse_sam(self):
for case in self.cases:
df = parse_sam(case.exp.sam)
df.to_csv(case.exp.sam_df, sep='\t', index=False)
df.to_csv(case.obs.sam_df, sep='\t', index=False)
self.assertTrue(
cmp(case.exp.sam_df, case.obs.sam_df, shallow=False))
def test_filter_best(self):
for case in self.cases:
df = parse_sam(case.exp.sam)
df_filter = filter_best(df)
df_filter.to_csv(case.exp.sam_best, sep='\t', index=False)
df_filter.to_csv(case.obs.sam_best, sep='\t', index=False)
self.assertTrue(
cmp(case.exp.sam_best, case.obs.sam_best, shallow=False))
def test_filter_ident_overlap(self):
for case in self.cases:
df = parse_sam(case.exp.sam)
df_filter = filter_ident_overlap(df, pident=90, overlap=5)
df_filter.to_csv(case.exp.sam_io5, sep='\t', index=False)
df_filter.to_csv(case.obs.sam_io5, sep='\t', index=False)
self.assertTrue(
cmp(case.exp.sam_io5, case.obs.sam_io5, shallow=False))
df_filter = filter_ident_overlap(df, pident=90, overlap=12)
df_filter.to_csv(case.exp.sam_io12, sep='\t', index=False)
df_filter.to_csv(case.obs.sam_io12, sep='\t', index=False)
self.assertTrue(
cmp(case.exp.sam_io12, case.obs.sam_io12, shallow=False))