def testFLT3_IandI(self): target = "./data/catalog/GRCh38/FLT3-ITD_exons_13-15.fa" args = Namespace(count=5, graphical=False, jellyfish_fn='./data/jf/03H112_IandI.jf', ratio=0.05, steps=500, target_fn=[target], verbose=False) with captured_output() as (out, err): fm.main_find_mut(args, None) output = out.getvalue() find_output = output.split("\n") find_output = find_output[16].split("\t") self.assertEqual(find_output[2], "ITD", "Test fail: FLT3-ITD -> find type") self.assertEqual( find_output[3], "152:/TCTTGCGTTCATCACTTTTCCAAAAGCACCTGATCCTAGTACCTTCCCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTC:152", "Test fail: FLT3-ITD -> find variant") self.assertEqual( find_output[8], "TTGAGACTCCTGTTTTGCTAATTCCATAAGCTGTTGCGTTCATCACTTTTCCAAAAGCACCTGATCCTAGTACCTTCCCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCTCTTGCGTTCATCACTTTTCCAAAAGCACCTGATCCTAGTACCTTCCCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTC", "Test fail: FLT3-ITD -> find sequence") args = Namespace(target=target, infile=StringIO(output), info="vs_ref", min_cov=1) with captured_output() as (out, err): fr.main_find_report(args, None) output = out.getvalue() report_output = output.split("\n") report_output = report_output[1].split("\t") self.assertEqual(report_output[2], "chr13:28034128", "Test fail: FLT3-ITD -> report pos") self.assertEqual(report_output[3], "I&I", "Test fail: FLT3-ITD -> report type") self.assertEqual( report_output[10], "/TCTTGCGTTCATCACTTTTCCAAAAGCACCTGATCCTAGTACCTTCCCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTC", "Test fail: FLT3-ITD -> report variant") self.assertEqual( report_output[13], "CTTTCAGCATTTTGACGGCAACCTGGATTGAGACTCCTGTTTTGCTAATTCCATAAGCTGTTGCGTTCATCACTTTTCCAAAAGCACCTGATCCTAGTACCTTCCCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCTCTTGCGTTCATCACTTTTCCAAAAGCACCTGATCCTAGTACCTTCCCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGTAGCTGGCTTTCATACCTAAATTGCTTTTTGTACTTGTGACAAATTAGCAGGGTTAAAACGACAATGAAGAGGAGACAAACACCAATTGTTGCATAGAATGAGATGTTGTCTTGGATGAAAGGGAAGGGGC", "Test fail: FLT3-ITD -> report sequence")
def testNPM1(self): target = "./data/catalog/GRCh38/NPM1_4ins_exons_10-11utr.fa" args = Namespace(count=5, graphical=False, jellyfish_fn='./data/jf/02H025_NPM1.jf', ratio=0.05, steps=500, target_fn=[target], verbose=False) with captured_output() as (out, err): fm.main_find_mut(args, None) output = out.getvalue() find_output = output.split("\n") find_output = find_output[16].split("\t") self.assertEqual(find_output[2], "Insertion", "Test fail: NPM1 -> find type") self.assertEqual(find_output[3], "45:/TCTG:45", "Test fail: NPM1 -> find variant") self.assertEqual( find_output[8], "CGGATGACTGACCAAGAGGCTATTCAAGATCTCTGTCTGGCAGTGGAGGAAGTCTCTTTAAGAAAATAG", "Test fail: NPM1 -> find sequence") args = Namespace(target=target, infile=StringIO(output), info="vs_ref", min_cov=1) with captured_output() as (out, err): fr.main_find_report(args, None) output = out.getvalue() report_output = output.split("\n") report_output = report_output[1].split("\t") self.assertEqual(report_output[2], "chr5:171410544", "Test fail: NPM1 -> report pos") self.assertEqual(report_output[3], "ITD", "Test fail: NPM1 -> report type") self.assertEqual(report_output[10], "/TCTG", "Test fail: NPM1 -> report variant") self.assertEqual( report_output[13], "AATTGCTTCCGGATGACTGACCAAGAGGCTATTCAAGATCTCTGTCTGGCAGTGGAGGAAGTCTCTTTAAGAAAATAGTTTAAA", "Test fail: NPM1 -> report sequence")
def testDNMT3A(self): target = "./data/catalog/GRCh38/DNMT3A_R882_exon_23.fa" args = Namespace(count=5, graphical=False, jellyfish_fn="./data/jf/02H033_DNMT3A_sub.jf", ratio=0.05, steps=500, target_fn=[target], verbose=False) with captured_output() as (out, err): fm.main_find_mut(args, None) output = out.getvalue() find_output = output.split("\n") find_output = find_output[16].split("\t") self.assertEqual(find_output[2], "Substitution", "Test fail: DNMT3A -> find type") self.assertEqual(find_output[3], "33:c/T:34", "Test fail: DNMT3A -> find variant") self.assertEqual( find_output[8], "TGACCGGCCCAGCAGTCTCTGCCTCGCCAAGTGGCTCATGTTGGAGACGTCAGTATAGTGGA", "Test fail: DNMT3A -> find sequence") args = Namespace(target=target, infile=StringIO(output), info="vs_ref", min_cov=1) with captured_output() as (out, err): fr.main_find_report(args, None) output = out.getvalue() report_output = output.split("\n") report_output = report_output[1].split("\t") self.assertEqual(report_output[2], "chr2:25234373", "Test fail: DNMT3A -> report pos") self.assertEqual(report_output[3], "Substitution", "Test fail: DNMT3A -> report type") self.assertEqual(report_output[10], "c/T", "Test fail: DNMT3A -> report variant") self.assertEqual( report_output[13], "ATGACCGGCCCAGCAGTCTCTGCCTCGCCAAGTGGCTCATGTTGGAGACGTCAGTATAGTGGACT", "Test fail: DNMT3A -> report sequence")
def testFLT3_TKD(self): target = "./data/catalog/GRCh38/FLT3-TKD_exon_20.fa" args = Namespace(count=5, graphical=False, jellyfish_fn='./data/jf/05H094_FLT3-TKD_del.jf', ratio=0.05, steps=500, target_fn=[target], verbose=False) with captured_output() as (out, err): fm.main_find_mut(args, None) output = out.getvalue() find_output = output.split("\n") find_output = find_output[16].split("\t") self.assertEqual(find_output[2], "Deletion", "Test fail: FLT3-TKD -> find type") self.assertEqual(find_output[3], "32:gat/:35", "Test fail: FLT3-TKD -> find variant") self.assertEqual( find_output[8], "TGCCCCTGACAACATAGTTGGAATCACTCATATCTCGAGCCAATCCAAAGTCACATATCTT", "Test fail: FLT3-TKD -> find sequence") args = Namespace(target=target, infile=StringIO(output), info="vs_ref", min_cov=1) with captured_output() as (out, err): fr.main_find_report(args, None) output = out.getvalue() report_output = output.split("\n") report_output = report_output[2].split("\t") self.assertEqual(report_output[2], "", "Test fail: FLT3-TKD -> report pos") self.assertEqual(report_output[3], "Deletion", "Test fail: FLT3-TKD -> report type") self.assertEqual(report_output[10], "gat/", "Test fail: FLT3-TKD -> report variant") self.assertEqual( report_output[13], "TGCCCCTGACAACATAGTTGGAATCACTCATATCTCGAGCCAATCCAAAGTCACATATCTTCACC", "Test fail: FLT3-TKD -> report sequence")
def test_DNMT3A(self): target = "./data/catalog/GRCh38/DNMT3A_R882_exon_23.fa" args = Namespace(count=5, graphical=False, jellyfish_fn="./data/jf/02H033_DNMT3A_sub.jf", ratio=0.05, steps=500, branchs=10, target_fn=[target], verbose=False) with captured_output() as (out, err): fm.main_find_mut(args, None) fm_output = out.getvalue() find_output = fm_output.split("\n") find_output = find_output[11].split("\t") self.assertEqual(find_output[2], "Substitution", "Test fail: DNMT3A -> find type") self.assertEqual(find_output[3], "33:c/T:34", "Test fail: DNMT3A -> find variant") self.assertEqual( find_output[8], "TGACCGGCCCAGCAGTCTCTGCCTCGCCAAGTGGCTCATGTTGGAGACGTCAGTATAGTGGA", "Test fail: DNMT3A -> find sequence") args = Namespace(target=target, infile=StringIO(fm_output), info="vs_ref", min_cov=1, exclu="", format=None) with captured_output() as (out, err): fr.main_find_report(args, None) output = out.getvalue() report_output = output.split("\n") report_output = report_output[2].split("\t") self.assertEqual(report_output[2], "chr2:25234373", "Test fail: DNMT3A -> report pos") self.assertEqual(report_output[3], "Substitution", "Test fail: DNMT3A -> report type") self.assertEqual(report_output[4], "1", "Test fail: DNMT3A -> report Removed") self.assertEqual(report_output[5], "1", "Test fail: DNMT3A -> report Added") self.assertEqual(report_output[6], "33.7", "Test fail: DNMT3A -> report Abnormal") self.assertEqual(report_output[7], "48.7", "Test fail: DNMT3A -> report Normal") self.assertEqual(report_output[8], "0.409", "Test fail: DNMT3A -> report rVAF") self.assertEqual(report_output[9], "32", "Test fail: DNMT3A -> report Min_coverage") self.assertEqual(report_output[11], "c/T", "Test fail: DNMT3A -> report variant") self.assertEqual( report_output[14], "ATGACCGGCCCAGCAGTCTCTGCCTCGCCAAGTGGCTCATGTTGGAGACGTCAGTATAGTGGACT", "Test fail: DNMT3A -> report sequence") args = Namespace(target=target, infile=StringIO(fm_output), info="vs_ref", min_cov=1, exclu="", format="vcf") with captured_output() as (out, err): fr.main_find_report(args, None) output = out.getvalue() report_output = [o for o in output.split("\n") if o and o[0] != "#"] report_output = report_output[0].split("\t") self.assertEqual(report_output[1], "25234373", "Test fail: DNMT3A -> vcf report pos") self.assertEqual(report_output[3], "C", "Test fail: DNMT3A -> vcf report ref") self.assertEqual(report_output[4], "T", "Test fail: DNMT3A -> vcf report alt")
def test_NPM1(self): target = "./data/catalog/GRCh38/NPM1_4ins_exons_10-11utr.fa" args = Namespace(count=5, graphical=False, jellyfish_fn='./data/jf/02H025_NPM1.jf', ratio=0.05, steps=500, branchs=10, target_fn=[target], verbose=False) with captured_output() as (out, err): fm.main_find_mut(args, None) fm_output = out.getvalue() find_output = fm_output.split("\n") find_output = find_output[11].split("\t") self.assertEqual(find_output[2], "Insertion", "Test fail: NPM1 -> find type") self.assertEqual(find_output[3], "45:/TCTG:45", "Test fail: NPM1 -> find variant") self.assertEqual( find_output[8], "CGGATGACTGACCAAGAGGCTATTCAAGATCTCTGTCTGGCAGTGGAGGAAGTCTCTTTAAGAAAATAG", "Test fail: NPM1 -> find sequence") args = Namespace(target=target, infile=StringIO(fm_output), info="vs_ref", min_cov=1, exclu="", format=None) with captured_output() as (out, err): fr.main_find_report(args, None) output = out.getvalue() report_output = output.split("\n") report_output = report_output[2].split("\t") self.assertEqual(report_output[2], "chr5:171410544", "Test fail: NPM1 -> report pos") self.assertEqual(report_output[3], "ITD", "Test fail: NPM1 -> report type") self.assertEqual(report_output[4], "0", "Test fail: NPM1 -> report Removed") self.assertEqual(report_output[5], "4 | 1", "Test fail: NPM1 -> report Added") self.assertEqual(report_output[6], "2870.6", "Test fail: NPM1 -> report Abnormal") self.assertEqual(report_output[7], "3055.2", "Test fail: NPM1 -> report Normal") self.assertEqual(report_output[8], "0.484", "Test fail: NPM1 -> report rVAF") self.assertEqual(report_output[9], "2428", "Test fail: NPM1 -> report Min_coverage") self.assertEqual(report_output[11], "/TCTG", "Test fail: NPM1 -> report variant") self.assertEqual( report_output[14], "AATTGCTTCCGGATGACTGACCAAGAGGCTATTCAAGATCTCTGTCTGGCAGTGGAGGAAGTCTCTTTAAGAAAATAGTTTAAA", "Test fail: NPM1 -> report sequence") args = Namespace(target=target, infile=StringIO(fm_output), info="vs_ref", min_cov=1, exclu="", format="vcf") with captured_output() as (out, err): fr.main_find_report(args, None) output = out.getvalue() report_output = [o for o in output.split("\n") if o and o[0] != "#"] report_output = report_output[0].split("\t") self.assertEqual(report_output[1], "171410539", "Test fail: NPM1 -> vcf report pos") self.assertEqual(report_output[3], "CTCTGG", "Test fail: NPM1 -> vcf report ref") self.assertEqual(report_output[4], "CTCTGTCTGG", "Test fail: NPM1 -> vcf report alt")
def test_FLT3_ITD(self): target = "./data/catalog/GRCh38/FLT3-ITD_exons_13-15.fa" args = Namespace(count=5, graphical=False, jellyfish_fn='./data/jf/03H116_ITD.jf', ratio=0.05, steps=500, branchs=10, target_fn=[target], verbose=False) with captured_output() as (out, err): fm.main_find_mut(args, None) fm_output = out.getvalue() find_output = fm_output.split("\n") find_output = find_output[11].split("\t") self.assertEqual(find_output[2], "ITD", "Test fail: FLT3-ITD -> find type") self.assertEqual( find_output[3], "204:/AACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACC:204", "Test fail: FLT3-ITD -> find variant") self.assertEqual( find_output[8], "TACCTTCCCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGA" + "AGTACTCATTATCTGAGGAGCCGGTCACCAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAG" + "TACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGTAGCTGGCTTTCATACCTA", "Test fail: FLT3-ITD -> find sequence") args = Namespace(target=target, infile=StringIO(fm_output), info="vs_ref", min_cov=1, exclu="", format=None) with captured_output() as (out, err): fr.main_find_report(args, None) output = out.getvalue() report_output = output.split("\n") report_output = report_output[2].split("\t") self.assertEqual(report_output[2], "chr13:28034180", "Test fail: FLT3-ITD -> report pos") self.assertEqual(report_output[3], "ITD", "Test fail: FLT3-ITD -> report type") self.assertEqual(report_output[4], "0", "Test fail: FLT3-ITD -> report Removed") self.assertEqual(report_output[5], "75 | 1", "Test fail: FLT3-ITD -> report Added") self.assertEqual(report_output[6], "417.6", "Test fail: FLT3-ITD -> report Abnormal") self.assertEqual(report_output[7], "1096.7", "Test fail: FLT3-ITD -> report Normal") self.assertEqual(report_output[8], "0.276", "Test fail: FLT3-ITD -> report rVAF") self.assertEqual(report_output[9], "443", "Test fail: FLT3-ITD -> report Min_coverage") self.assertEqual( report_output[11], "/AACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACC", "Test fail: FLT3-ITD -> report variant") self.assertEqual( report_output[14], "CTTTCAGCATTTTGACGGCAACCTGGATTGAGACTCCTGTTTTGCTAATTCCATAAGCTGTTGCGTTCATCACTTTT" + "CCAAAAGCACCTGATCCTAGTACCTTCCCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATA" + "TTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCAACTCCCATTTGAGATCATATTCATATT" + "CTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGTAGCTGGCTTTCATACCTA" + "AATTGCTTTTTGTACTTGTGACAAATTAGCAGGGTTAAAACGACAATGAAGAGGAGACAAACACCAATTGTTGCATA" + "GAATGAGATGTTGTCTTGGATGAAAGGGAAGGGGC", "Test fail: FLT3-ITD -> report sequence") args = Namespace(target=target, infile=StringIO(fm_output), info="vs_ref", min_cov=1, exclu="", format="vcf") with captured_output() as (out, err): fr.main_find_report(args, None) output = out.getvalue() report_output = [o for o in output.split("\n") if o and o[0] != "#"] report_output = report_output[0].split("\t") self.assertEqual(report_output[1], "28034104", "Test fail: FLT3-ITD -> vcf report pos") self.assertEqual( report_output[3], "AAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCT", "Test fail: FLT3-ITD -> vcf report ref") self.assertEqual( report_output[4], "AAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCA" + "ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCT", "Test fail: FLT3-ITD -> vcf report alt")
def test_FLT3_IandI(self): target = "./data/catalog/GRCh38/FLT3-ITD_exons_13-15.fa" args = Namespace(count=5, graphical=False, jellyfish_fn='./data/jf/03H112_IandI.jf', ratio=0.05, steps=500, branchs=10, target_fn=[target], verbose=False) with captured_output() as (out, err): fm.main_find_mut(args, None) fm_output = out.getvalue() find_output = fm_output.split("\n") find_output = find_output[11].split("\t") self.assertEqual(find_output[2], "ITD", "Test fail: FLT3-IandI -> find type") self.assertEqual( find_output[3], "152:/TCTTGCGTTCATCACTTTTCCAAAAGCACCTGATCCTAGTACCTTCCCAAACTCTAAATTTTCTCTTGGAA" + "ACTCCCATTTGAGATCATATTC:152", "Test fail: FLT3-IandI -> find variant") self.assertEqual( find_output[8], "TTGAGACTCCTGTTTTGCTAATTCCATAAGCTGTTGCGTTCATCACTTTTCCAAAAGCACCTGATCCTAGTACCTTC" + "CCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCTCTTGCGTTCATCACTTTTCCAAAAGCACC" + "TGATCCTAGTACCTTCCCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAAT" + "CAACGTAGAAGTACTC", "Test fail: FLT3-IandI -> find sequence") args = Namespace(target=target, infile=StringIO(fm_output), info="vs_ref", min_cov=1, exclu="", format=None) with captured_output() as (out, err): fr.main_find_report(args, None) output = out.getvalue() report_output = output.split("\n") report_output = report_output[2].split("\t") self.assertEqual(report_output[2], "chr13:28034128", "Test fail: FLT3-IandI -> report pos") self.assertEqual(report_output[3], "I&I", "Test fail: FLT3-IandI -> report type") self.assertEqual(report_output[4], "0", "Test fail: FLT3-IandI -> report Removed") self.assertEqual(report_output[5], "93 | 1", "Test fail: FLT3-IandI -> report Added") self.assertEqual(report_output[6], "399.1", "Test fail: FLT3-IandI -> report Abnormal") self.assertEqual(report_output[7], "398.5", "Test fail: FLT3-IandI -> report Normal") self.assertEqual(report_output[8], "0.500", "Test fail: FLT3-IandI -> report rVAF") self.assertEqual(report_output[9], "285", "Test fail: FLT3-IandI -> report Min_coverage") self.assertEqual( report_output[11], "/TCTTGCGTTCATCACTTTTCCAAAAGCACCTGATCCTAGTACCTTCCCAAACTCTAAATTTTCTCTTGGAAACTCC" + "CATTTGAGATCATATTC", "Test fail: FLT3-IandI -> report variant") self.assertEqual( report_output[14], "CTTTCAGCATTTTGACGGCAACCTGGATTGAGACTCCTGTTTTGCTAATTCCATAAGCTGTTGCGTTCATCACTTTT" + "CCAAAAGCACCTGATCCTAGTACCTTCCCAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCTCT" + "TGCGTTCATCACTTTTCCAAAAGCACCTGATCCTAGTACCTTCCCAAACTCTAAATTTTCTCTTGGAAACTCCCATT" + "TGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATCTGT" + "AGCTGGCTTTCATACCTAAATTGCTTTTTGTACTTGTGACAAATTAGCAGGGTTAAAACGACAATGAAGAGGAGACA" + "AACACCAATTGTTGCATAGAATGAGATGTTGTCTTGGATGAAAGGGAAGGGGC", "Test fail: FLT3-IandI -> report sequence") args = Namespace(target=target, infile=StringIO(fm_output), info="vs_ref", min_cov=1, exclu="", format="vcf") with captured_output() as (out, err): fr.main_find_report(args, None) output = err.getvalue() find_output = [o for o in output.split("\n") if o[:5] == "NOTE:"] find_output = find_output[0] self.assertEqual( find_output, "NOTE: Mutation overlaps 2 exons or more, VCF output is disabled ")
def test_FLT3_TKD(self): target = "./data/catalog/GRCh38/FLT3-TKD_exon_20.fa" args = Namespace(count=5, graphical=False, jellyfish_fn='./data/jf/05H094_FLT3-TKD_del.jf', ratio=0.05, steps=500, branchs=10, nodes=10000, target_fn=[target], verbose=False, debug=False) with captured_output() as (out, err): fm.main_find_mut(args, None) fm_output = out.getvalue() find_output = fm_output.split("\n") find_output = find_output[13].split("\t") self.assertEqual(find_output[2], "Deletion", "Test fail: FLT3-TKD -> find type") self.assertEqual(find_output[3], "32:gat/:35", "Test fail: FLT3-TKD -> find variant") self.assertEqual( find_output[8], "TGCCCCTGACAACATAGTTGGAATCACTCATATCTCGAGCCAATCCAAAGTCACATATCTT", "Test fail: FLT3-TKD -> find sequence") args = Namespace(target=target, infile=StringIO(fm_output), info="vs_ref", min_cov=1, exclu="", format=None) with captured_output() as (out, err): fr.main_find_report(args, None) output = out.getvalue() report_output = output.split("\n") report_output = report_output[2].split("\t") self.assertEqual(report_output[2], "", "Test fail: FLT3-TKD -> report pos") self.assertEqual(report_output[3], "Deletion", "Test fail: FLT3-TKD -> report type") self.assertEqual(report_output[11], "gat/", "Test fail: FLT3-TKD -> report variant") self.assertEqual( report_output[14], "TGCCCCTGACAACATAGTTGGAATCACTCATATCTCGAGCCAATCCAAAGTCACATATCTTCACC", "Test fail: FLT3-TKD -> report sequence") args = Namespace(target=target, infile=StringIO(fm_output), info="vs_ref", min_cov=1, exclu="", format="vcf") with captured_output() as (out, err): fr.main_find_report(args, None) output = out.getvalue() report_output = [o for o in output.split("\n") if o and o[0] != "#"] report_output = report_output[0].split("\t") self.assertEqual(report_output[1], "28018497", "Test fail: FLT3-TKD -> vcf report pos") self.assertEqual(report_output[3], "CATGATA", "Test fail: FLT3-TKD -> vcf report ref") self.assertEqual(report_output[4], "CATA", "Test fail: FLT3-TKD -> vcf report alt")