def test_merge_srna_gff(self): out_file = os.path.join(self.test_folder, "test_out") gen_file(os.path.join(self.test_folder, "aaa.gff"), self.example.gff_file) ms.read_gff = Mock_func().mock_read_gff gffs = {"merge": out_file, "utr": "UTR", "normal": "inter"} ms.merge_srna_gff(gffs, False, 0.5, os.path.join(self.test_folder, "aaa.gff")) datas, attributes = extract_info(out_file, "file") self.assertListEqual(datas, [ 'aaa\tANNOgesic\tncRNA\t54\t254\t.\t+\t.', 'aaa\tANNOgesic\tncRNA\t54\t254\t.\t+\t.' ]) self.assertEqual( set(attributes[0]), set([ 'overlap_percent=NA', 'end_cleavage=cleavage_40', 'start_cleavage=cleavage_4', 'Name=sRNA_00000', 'with_TSS=TSS_3', 'ID=srna0', 'sRNA_type=interCDS', 'overlap_cds=NA' ])) self.assertEqual( set(attributes[1]), set([ 'overlap_percent=NA', 'end_cleavage=NA', 'Name=sRNA_00001', 'with_TSS=NA', 'ID=srna1', 'sRNA_type=intergenic', 'overlap_cds=NA' ]))
def _merge_srna(self, args_srna, gffs, csvs, prefix, gff_file, tss, tex_datas): print("merging data of sRNA...") merge_srna_gff(gffs, args_srna.in_cds, args_srna.cutoff_overlap, gff_file) merge_srna_table(gffs["merge"], csvs, tex_datas[2], tex_datas[3], tss, args_srna)
def _merge_srna(self, args_srna, gffs, csvs, prefix, gff_file, tss): print("merging data of intergenic and UTR_derived sRNA...") merge_srna_gff(gffs, args_srna.in_cds, args_srna.cutoff_overlap, gff_file) merge_srna_table(gffs["merge"], csvs, os.path.join(args_srna.wig_path, "_".join([prefix, "forward.wig"])), os.path.join(args_srna.wig_path, "_".join([prefix, "reverse.wig"])), tss, args_srna)
def test_merge_srna_gff(self): out_file = os.path.join(self.test_folder, "test_out") gen_file(os.path.join(self.test_folder, "aaa.gff"), self.example.gff_file) ms.read_gff = Mock_func().mock_read_gff gffs = {"merge": out_file, "utr": "UTR", "normal": "inter"} ms.merge_srna_gff(gffs, False, 0.5, os.path.join(self.test_folder, "aaa.gff"), False) datas, attributes = extract_info(out_file, "file") self.assertListEqual(datas, ['aaa\tANNOgesic\tncRNA\t54\t254\t.\t+\t.']) self.assertEqual(set(attributes[0]), set(['overlap_cds=NA', 'Name=sRNA_00000', 'ID=aaa_srna0', 'sRNA_type=intergenic', 'end_cleavage=cleavage_40', 'with_TSS=TSS_3', 'overlap_percent=NA']))