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))