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")