def _check_results(self): self._check_no_error_results() from_gtf_ri_path = os.path.join(self._out_dir, 'fromGTF.RI.txt') from_gtf_ri_header, from_gtf_ri_rows, error = output_parser.parse_from_gtf( from_gtf_ri_path) self.assertFalse(error) self.assertEqual(len(from_gtf_ri_rows), 3) sorted_from_gtf_ri_rows = self._sort_by_event_coords(from_gtf_ri_rows) self._check_event_coords(sorted_from_gtf_ri_rows[0], '0', '98', '200', '300') self._check_event_coords(sorted_from_gtf_ri_rows[1], '0', '100', '200', '300') self._check_event_coords(sorted_from_gtf_ri_rows[2], '0', '100', '202', '300') from_gtf_novel_junction_ri_path = os.path.join( self._out_dir, 'fromGTF.novelJunction.RI.txt') from_gtf_novel_junction_ri_header, from_gtf_novel_junction_ri_rows, error = output_parser.parse_from_gtf_novel_junction( from_gtf_novel_junction_ri_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_junction_ri_rows), 0) from_gtf_novel_splice_site_ri_path = os.path.join( self._out_dir, 'fromGTF.novelSpliceSite.RI.txt') from_gtf_novel_splice_site_ri_header, from_gtf_novel_splice_site_ri_rows, error = output_parser.parse_from_gtf_novel_splice_site( from_gtf_novel_splice_site_ri_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_splice_site_ri_rows), 2) sorted_from_gtf_novel_splice_site_ri_rows = self._sort_by_event_coords( from_gtf_novel_splice_site_ri_rows) self._check_event_coords(sorted_from_gtf_novel_splice_site_ri_rows[0], '0', '98', '200', '300') self._check_event_coords(sorted_from_gtf_novel_splice_site_ri_rows[1], '0', '100', '202', '300')
def _check_results(self): self._check_no_error_results() from_gtf_se_path = os.path.join(self._out_dir, 'fromGTF.SE.txt') from_gtf_se_header, from_gtf_se_rows, error = ( output_parser.parse_from_gtf(from_gtf_se_path)) self.assertFalse(error) self.assertEqual(len(from_gtf_se_rows), 1) self._check_event_coords(from_gtf_se_rows[0], '200', '300', '400', '500', '600', '700') from_gtf_novel_junction_se_path = os.path.join( self._out_dir, 'fromGTF.novelJunction.SE.txt') (from_gtf_novel_junction_se_header, from_gtf_novel_junction_se_rows, error) = output_parser.parse_from_gtf_novel_junction( from_gtf_novel_junction_se_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_junction_se_rows), 0) from_gtf_novel_splice_site_se_path = os.path.join( self._out_dir, 'fromGTF.novelSpliceSite.SE.txt') (from_gtf_novel_splice_site_se_header, from_gtf_novel_splice_site_se_rows, error) = output_parser.parse_from_gtf_novel_splice_site( from_gtf_novel_splice_site_se_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_splice_site_se_rows), 0)
def _check_results(self): self._check_no_error_results() from_gtf_a3ss_path = os.path.join(self._out_dir, 'fromGTF.A3SS.txt') from_gtf_a3ss_header, from_gtf_a3ss_rows, error = output_parser.parse_from_gtf( from_gtf_a3ss_path) self.assertFalse(error) self.assertEqual(len(from_gtf_a3ss_rows), 7) sorted_from_gtf_a3ss_rows = self._sort_by_event_coords( from_gtf_a3ss_rows) self._check_event_coords(sorted_from_gtf_a3ss_rows[0], '0', '94', '200', '300', '400') self._check_event_coords(sorted_from_gtf_a3ss_rows[1], '0', '100', '200', '202', '400') self._check_event_coords(sorted_from_gtf_a3ss_rows[2], '0', '100', '200', '300', '400') self._check_event_coords(sorted_from_gtf_a3ss_rows[3], '0', '100', '200', '302', '400') self._check_event_coords(sorted_from_gtf_a3ss_rows[4], '0', '100', '202', '300', '400') self._check_event_coords(sorted_from_gtf_a3ss_rows[5], '0', '100', '202', '302', '400') self._check_event_coords(sorted_from_gtf_a3ss_rows[6], '0', '100', '300', '302', '400') from_gtf_novel_junction_a3ss_path = os.path.join( self._out_dir, 'fromGTF.novelJunction.A3SS.txt') from_gtf_novel_junction_a3ss_header, from_gtf_novel_junction_a3ss_rows, error = output_parser.parse_from_gtf_novel_junction( from_gtf_novel_junction_a3ss_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_junction_a3ss_rows), 0) from_gtf_novel_splice_site_a3ss_path = os.path.join( self._out_dir, 'fromGTF.novelSpliceSite.A3SS.txt') from_gtf_novel_splice_site_a3ss_header, from_gtf_novel_splice_site_a3ss_rows, error = output_parser.parse_from_gtf_novel_splice_site( from_gtf_novel_splice_site_a3ss_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_splice_site_a3ss_rows), 6) sorted_from_gtf_novel_splice_site_a3ss_rows = self._sort_by_event_coords( from_gtf_novel_splice_site_a3ss_rows) self._check_event_coords( sorted_from_gtf_novel_splice_site_a3ss_rows[0], '0', '94', '200', '300', '400') self._check_event_coords( sorted_from_gtf_novel_splice_site_a3ss_rows[1], '0', '100', '200', '202', '400') self._check_event_coords( sorted_from_gtf_novel_splice_site_a3ss_rows[2], '0', '100', '200', '302', '400') self._check_event_coords( sorted_from_gtf_novel_splice_site_a3ss_rows[3], '0', '100', '202', '300', '400') self._check_event_coords( sorted_from_gtf_novel_splice_site_a3ss_rows[4], '0', '100', '202', '302', '400') self._check_event_coords( sorted_from_gtf_novel_splice_site_a3ss_rows[5], '0', '100', '300', '302', '400')
def _check_results_post(self): self._check_no_error_results() command_stdout_file_name = self._get_stdout_file_name() with open(command_stdout_file_name, 'rt') as out_f_h: out_lines = out_f_h.readlines() tests.util.assert_some_line_has(self, out_lines, 'Processing count files') from_gtf_se_path = os.path.join(self._out_dir, 'fromGTF.SE.txt') from_gtf_se_header, from_gtf_se_rows, error = output_parser.parse_from_gtf( from_gtf_se_path) self.assertFalse(error) self.assertEqual(len(from_gtf_se_rows), 1) from_gtf_se_row = from_gtf_se_rows[0] self.assertEqual(from_gtf_se_row['GeneID'], tests.util.double_quote(tests.util.gene_id_str(1))) self.assertEqual(from_gtf_se_row['exonStart_0base'], '200') self.assertEqual(from_gtf_se_row['exonEnd'], '300') jc_raw_se_path = os.path.join(self._out_dir, 'JC.raw.input.SE.txt') jc_raw_se_header, jc_raw_se_rows, error = output_parser.parse_jc_raw( jc_raw_se_path) self.assertFalse(error) self.assertEqual(len(jc_raw_se_rows), 1) jc_raw_se_row = jc_raw_se_rows[0] self.assertEqual(jc_raw_se_row['ID'], from_gtf_se_row['ID']) self.assertEqual(jc_raw_se_row['IJC_SAMPLE_1'], '1,1') self.assertEqual(jc_raw_se_row['SJC_SAMPLE_1'], '0,0') self.assertEqual(jc_raw_se_row['IJC_SAMPLE_2'], '0,0') self.assertEqual(jc_raw_se_row['SJC_SAMPLE_2'], '1,1') se_mats_jc_path = os.path.join(self._out_dir, 'SE.MATS.JC.txt') se_mats_jc_header, se_mats_jc_rows, error = output_parser.parse_mats_jc( se_mats_jc_path) self.assertFalse(error) self._check_se_mats_jc_header(se_mats_jc_header) self.assertEqual(len(se_mats_jc_rows), 1) se_mats_jc_row = se_mats_jc_rows[0] pvalue = float(se_mats_jc_row['PValue']) tests.util.assert_within_bounds(self, pvalue, 0, 1) fdr = float(se_mats_jc_row['FDR']) tests.util.assert_within_bounds(self, fdr, 0, 1) inc_level_1_splits = se_mats_jc_row['IncLevel1'].split(',') self.assertEqual(len(inc_level_1_splits), 2) self.assertAlmostEqual(float(inc_level_1_splits[0]), 1) self.assertAlmostEqual(float(inc_level_1_splits[1]), 1) inc_level_2_splits = se_mats_jc_row['IncLevel2'].split(',') self.assertEqual(len(inc_level_2_splits), 2) self.assertAlmostEqual(float(inc_level_2_splits[0]), 0) self.assertAlmostEqual(float(inc_level_2_splits[1]), 0) self.assertAlmostEqual(float(se_mats_jc_row['IncLevelDifference']), 1)
def _check_results(self): self._check_no_error_results() from_gtf_mxe_path = os.path.join(self._out_dir, 'fromGTF.MXE.txt') from_gtf_mxe_header, from_gtf_mxe_rows, error = output_parser.parse_from_gtf( from_gtf_mxe_path) self.assertFalse(error) self.assertEqual(len(from_gtf_mxe_rows), 5) sorted_from_gtf_mxe_rows = self._sort_by_event_coords( from_gtf_mxe_rows) self._check_event_coords(sorted_from_gtf_mxe_rows[0], '0', '100', '200', '300', '400', '500', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[1], '1600', '1700', '1800', '1900', '2000', '2100', '2200', '2300') self._check_event_coords(sorted_from_gtf_mxe_rows[2], '3200', '3300', '3400', '3500', '3600', '3700', '4000', '4100') self._check_event_coords(sorted_from_gtf_mxe_rows[3], '4200', '4300', '4600', '4700', '4800', '4900', '5000', '5100') self._check_event_coords(sorted_from_gtf_mxe_rows[4], '5200', '5300', '5400', '5500', '5600', '5700', '5800', '5900') from_gtf_novel_junction_mxe_path = os.path.join( self._out_dir, 'fromGTF.novelJunction.MXE.txt') from_gtf_novel_junction_mxe_header, from_gtf_novel_junction_mxe_rows, error = output_parser.parse_from_gtf_novel_junction( from_gtf_novel_junction_mxe_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_junction_mxe_rows), 4) sorted_from_gtf_novel_junction_mxe_rows = self._sort_by_event_coords( from_gtf_novel_junction_mxe_rows) self._check_event_coords(sorted_from_gtf_novel_junction_mxe_rows[0], '1600', '1700', '1800', '1900', '2000', '2100', '2200', '2300') self._check_event_coords(sorted_from_gtf_novel_junction_mxe_rows[1], '3200', '3300', '3400', '3500', '3600', '3700', '4000', '4100') self._check_event_coords(sorted_from_gtf_novel_junction_mxe_rows[2], '4200', '4300', '4600', '4700', '4800', '4900', '5000', '5100') self._check_event_coords(sorted_from_gtf_novel_junction_mxe_rows[3], '5200', '5300', '5400', '5500', '5600', '5700', '5800', '5900') from_gtf_novel_splice_site_mxe_path = os.path.join( self._out_dir, 'fromGTF.novelSpliceSite.MXE.txt') from_gtf_novel_splice_site_mxe_header, from_gtf_novel_splice_site_mxe_rows, error = output_parser.parse_from_gtf_novel_splice_site( from_gtf_novel_splice_site_mxe_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_splice_site_mxe_rows), 0)
def _check_results(self): self._check_no_error_results() from_gtf_se_path = os.path.join(self._out_dir, 'fromGTF.SE.txt') from_gtf_se_header, from_gtf_se_rows, error = output_parser.parse_from_gtf( from_gtf_se_path) self.assertFalse(error) self.assertEqual(len(from_gtf_se_rows), 7) sorted_from_gtf_se_rows = self._sort_by_event_coords(from_gtf_se_rows) self._check_event_coords(sorted_from_gtf_se_rows[0], '0', '96', '200', '300', '400', '500') self._check_event_coords(sorted_from_gtf_se_rows[1], '0', '100', '200', '298', '400', '500') self._check_event_coords(sorted_from_gtf_se_rows[2], '0', '100', '200', '300', '400', '500') self._check_event_coords(sorted_from_gtf_se_rows[3], '0', '100', '200', '300', '404', '500') self._check_event_coords(sorted_from_gtf_se_rows[4], '0', '100', '202', '298', '400', '500') self._check_event_coords(sorted_from_gtf_se_rows[5], '0', '100', '202', '300', '400', '500') self._check_event_coords(sorted_from_gtf_se_rows[6], '600', '700', '800', '900', '1000', '1100') from_gtf_novel_junction_se_path = os.path.join( self._out_dir, 'fromGTF.novelJunction.SE.txt') from_gtf_novel_junction_se_header, from_gtf_novel_junction_se_rows, error = output_parser.parse_from_gtf_novel_junction( from_gtf_novel_junction_se_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_junction_se_rows), 1) self._check_event_coords(from_gtf_novel_junction_se_rows[0], '600', '700', '800', '900', '1000', '1100') from_gtf_novel_splice_site_se_path = os.path.join( self._out_dir, 'fromGTF.novelSpliceSite.SE.txt') from_gtf_novel_splice_site_se_header, from_gtf_novel_splice_site_se_rows, error = output_parser.parse_from_gtf_novel_splice_site( from_gtf_novel_splice_site_se_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_splice_site_se_rows), 5) sorted_from_gtf_novel_splice_site_se_rows = self._sort_by_event_coords( from_gtf_novel_splice_site_se_rows) self._check_event_coords(sorted_from_gtf_novel_splice_site_se_rows[0], '0', '96', '200', '300', '400', '500') self._check_event_coords(sorted_from_gtf_novel_splice_site_se_rows[1], '0', '100', '200', '298', '400', '500') self._check_event_coords(sorted_from_gtf_novel_splice_site_se_rows[2], '0', '100', '200', '300', '404', '500') self._check_event_coords(sorted_from_gtf_novel_splice_site_se_rows[3], '0', '100', '202', '298', '400', '500') self._check_event_coords(sorted_from_gtf_novel_splice_site_se_rows[4], '0', '100', '202', '300', '400', '500')
def _check_results(self): self._check_no_error_results() se_mats_jc_path = os.path.join(self._out_dir, 'SE.MATS.JC.txt') se_mats_jc_header, se_mats_jc_rows, error = output_parser.parse_mats_jc( se_mats_jc_path) self.assertFalse(error) self._check_se_mats_jc_header(se_mats_jc_header) self.assertEqual(len(se_mats_jc_rows), 2) expected_genes = [ tests.util.double_quote(tests.util.gene_id_str(i)) for i in [1, 2] ] for row in se_mats_jc_rows: self.assertIn(row['exonStart_0base'], ['200', '1200']) if row['exonStart_0base'] == '200': self.assertEqual(row['IJC_SAMPLE_1'], '1,0') self.assertEqual(row['SJC_SAMPLE_1'], '1,0') self.assertIn(row['GeneID'], expected_genes) elif row['exonStart_0base'] == '1200': self.assertEqual(row['IJC_SAMPLE_1'], '0,1') self.assertEqual(row['SJC_SAMPLE_1'], '0,1') self.assertEqual(row['GeneID'], expected_genes[0]) from_gtf_se_path = os.path.join(self._out_dir, 'fromGTF.SE.txt') from_gtf_se_header, from_gtf_se_rows, error = ( output_parser.parse_from_gtf(from_gtf_se_path)) self.assertFalse(error) self.assertEqual(len(from_gtf_se_rows), 2) gtf_coords = list() for row in from_gtf_se_rows: gtf_coords.append(row['exonStart_0base']) self.assertEqual(sorted(gtf_coords), ['1200', '200']) from_gtf_nj_se_path = os.path.join(self._out_dir, 'fromGTF.novelJunction.SE.txt') from_gtf_nj_se_header, from_gtf_nj_se_rows, error = ( output_parser.parse_from_gtf_novel_junction(from_gtf_nj_se_path)) self.assertFalse(error) self.assertEqual(len(from_gtf_nj_se_rows), 0)
def _check_results(self): self._check_no_error_results() command_stdout_file_name = self._get_stdout_file_name() with open(command_stdout_file_name, 'rt') as out_f_h: out_lines = out_f_h.readlines() tests.util.assert_some_line_has(self, out_lines, 'Found 1 exon skipping event') from_gtf_se_path = os.path.join(self._out_dir, 'fromGTF.SE.txt') from_gtf_se_header, from_gtf_se_rows, error = output_parser.parse_from_gtf( from_gtf_se_path) self.assertFalse(error) self.assertEqual(len(from_gtf_se_rows), 1) from_gtf_se_row = from_gtf_se_rows[0] self.assertEqual(from_gtf_se_row['GeneID'], tests.util.double_quote(tests.util.gene_id_str(1))) self.assertEqual(from_gtf_se_row['geneSymbol'], tests.util.double_quote(tests.util.gene_name_str(1))) self.assertEqual(from_gtf_se_row['chr'], 'chr1') self.assertEqual(from_gtf_se_row['strand'], '+') self.assertEqual(from_gtf_se_row['exonStart_0base'], '200') self.assertEqual(from_gtf_se_row['exonEnd'], '300') self.assertEqual(from_gtf_se_row['upstreamES'], '0') self.assertEqual(from_gtf_se_row['upstreamEE'], '100') self.assertEqual(from_gtf_se_row['downstreamES'], '400') self.assertEqual(from_gtf_se_row['downstreamEE'], '500') jc_raw_se_path = os.path.join(self._out_dir, 'JC.raw.input.SE.txt') jc_raw_se_header, jc_raw_se_rows, error = output_parser.parse_jc_raw( jc_raw_se_path) self.assertFalse(error) self.assertEqual(len(jc_raw_se_rows), 1) jc_raw_se_row = jc_raw_se_rows[0] self.assertEqual(jc_raw_se_row['ID'], from_gtf_se_row['ID']) self.assertEqual(jc_raw_se_row['IJC_SAMPLE_1'], '1,1') self.assertEqual(jc_raw_se_row['SJC_SAMPLE_1'], '0,0') self.assertEqual(jc_raw_se_row['IJC_SAMPLE_2'], '0,0') self.assertEqual(jc_raw_se_row['SJC_SAMPLE_2'], '1,1')
def _check_results(self): self._check_no_error_results() from_gtf_a5ss_path = os.path.join(self._out_dir, 'fromGTF.A5SS.txt') from_gtf_a5ss_header, from_gtf_a5ss_rows, error = output_parser.parse_from_gtf( from_gtf_a5ss_path) self.assertFalse(error) self.assertEqual(len(from_gtf_a5ss_rows), 3) sorted_from_gtf_a5ss_rows = self._sort_by_event_coords( from_gtf_a5ss_rows) self._check_event_coords(sorted_from_gtf_a5ss_rows[0], '0', '100', '200', '300', '400') self._check_event_coords(sorted_from_gtf_a5ss_rows[1], '500', '600', '700', '800', '900') self._check_event_coords(sorted_from_gtf_a5ss_rows[2], '1000', '1100', '1200', '1300', '1400') from_gtf_novel_junction_a5ss_path = os.path.join( self._out_dir, 'fromGTF.novelJunction.A5SS.txt') from_gtf_novel_junction_a5ss_header, from_gtf_novel_junction_a5ss_rows, error = output_parser.parse_from_gtf_novel_junction( from_gtf_novel_junction_a5ss_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_junction_a5ss_rows), 2) sorted_from_gtf_novel_junction_a5ss_rows = self._sort_by_event_coords( from_gtf_novel_junction_a5ss_rows) self._check_event_coords(sorted_from_gtf_novel_junction_a5ss_rows[0], '500', '600', '700', '800', '900') self._check_event_coords(sorted_from_gtf_novel_junction_a5ss_rows[1], '1000', '1100', '1200', '1300', '1400') from_gtf_novel_splice_site_a5ss_path = os.path.join( self._out_dir, 'fromGTF.novelSpliceSite.A5SS.txt') from_gtf_novel_splice_site_a5ss_header, from_gtf_novel_splice_site_a5ss_rows, error = output_parser.parse_from_gtf_novel_splice_site( from_gtf_novel_splice_site_a5ss_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_splice_site_a5ss_rows), 0)
def _get_sorted_from_gtf_se_rows(self): from_gtf_se_path = os.path.join(self._out_dir, 'fromGTF.SE.txt') from_gtf_se_header, from_gtf_se_rows, error = output_parser.parse_from_gtf( from_gtf_se_path) self.assertFalse(error) return sorted(from_gtf_se_rows, key=lambda r: r['exonEnd'])
def _check_results(self): self._check_no_error_results() from_gtf_mxe_path = os.path.join(self._out_dir, 'fromGTF.MXE.txt') from_gtf_mxe_header, from_gtf_mxe_rows, error = output_parser.parse_from_gtf( from_gtf_mxe_path) self.assertFalse(error) self.assertEqual(len(from_gtf_mxe_rows), 16) sorted_from_gtf_mxe_rows = self._sort_by_event_coords( from_gtf_mxe_rows) self._check_event_coords(sorted_from_gtf_mxe_rows[0], '0', '100', '200', '298', '400', '498', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[1], '0', '100', '200', '298', '400', '500', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[2], '0', '100', '200', '298', '402', '498', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[3], '0', '100', '200', '298', '402', '500', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[4], '0', '100', '200', '300', '400', '498', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[5], '0', '100', '200', '300', '400', '500', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[6], '0', '100', '200', '300', '402', '498', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[7], '0', '100', '200', '300', '402', '500', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[8], '0', '100', '202', '298', '400', '498', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[9], '0', '100', '202', '298', '400', '500', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[10], '0', '100', '202', '298', '402', '498', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[11], '0', '100', '202', '298', '402', '500', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[12], '0', '100', '202', '300', '400', '498', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[13], '0', '100', '202', '300', '400', '500', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[14], '0', '100', '202', '300', '402', '498', '600', '700') self._check_event_coords(sorted_from_gtf_mxe_rows[15], '0', '100', '202', '300', '402', '500', '600', '700') from_gtf_novel_junction_mxe_path = os.path.join( self._out_dir, 'fromGTF.novelJunction.MXE.txt') from_gtf_novel_junction_mxe_header, from_gtf_novel_junction_mxe_rows, error = output_parser.parse_from_gtf_novel_junction( from_gtf_novel_junction_mxe_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_junction_mxe_rows), 0) from_gtf_novel_splice_site_mxe_path = os.path.join( self._out_dir, 'fromGTF.novelSpliceSite.MXE.txt') from_gtf_novel_splice_site_mxe_header, from_gtf_novel_splice_site_mxe_rows, error = output_parser.parse_from_gtf_novel_splice_site( from_gtf_novel_splice_site_mxe_path) self.assertFalse(error) self.assertEqual(len(from_gtf_novel_splice_site_mxe_rows), 15) sorted_from_gtf_novel_splice_site_mxe_rows = self._sort_by_event_coords( from_gtf_novel_splice_site_mxe_rows) self._check_event_coords(sorted_from_gtf_novel_splice_site_mxe_rows[0], '0', '100', '200', '298', '400', '498', '600', '700') self._check_event_coords(sorted_from_gtf_novel_splice_site_mxe_rows[1], '0', '100', '200', '298', '400', '500', '600', '700') self._check_event_coords(sorted_from_gtf_novel_splice_site_mxe_rows[2], '0', '100', '200', '298', '402', '498', '600', '700') self._check_event_coords(sorted_from_gtf_novel_splice_site_mxe_rows[3], '0', '100', '200', '298', '402', '500', '600', '700') self._check_event_coords(sorted_from_gtf_novel_splice_site_mxe_rows[4], '0', '100', '200', '300', '400', '498', '600', '700') self._check_event_coords(sorted_from_gtf_novel_splice_site_mxe_rows[5], '0', '100', '200', '300', '402', '498', '600', '700') self._check_event_coords(sorted_from_gtf_novel_splice_site_mxe_rows[6], '0', '100', '200', '300', '402', '500', '600', '700') self._check_event_coords(sorted_from_gtf_novel_splice_site_mxe_rows[7], '0', '100', '202', '298', '400', '498', '600', '700') self._check_event_coords(sorted_from_gtf_novel_splice_site_mxe_rows[8], '0', '100', '202', '298', '400', '500', '600', '700') self._check_event_coords(sorted_from_gtf_novel_splice_site_mxe_rows[9], '0', '100', '202', '298', '402', '498', '600', '700') self._check_event_coords( sorted_from_gtf_novel_splice_site_mxe_rows[10], '0', '100', '202', '298', '402', '500', '600', '700') self._check_event_coords( sorted_from_gtf_novel_splice_site_mxe_rows[11], '0', '100', '202', '300', '400', '498', '600', '700') self._check_event_coords( sorted_from_gtf_novel_splice_site_mxe_rows[12], '0', '100', '202', '300', '400', '500', '600', '700') self._check_event_coords( sorted_from_gtf_novel_splice_site_mxe_rows[13], '0', '100', '202', '300', '402', '498', '600', '700') self._check_event_coords( sorted_from_gtf_novel_splice_site_mxe_rows[14], '0', '100', '202', '300', '402', '500', '600', '700')