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Adjust 2020A microtest sample to stop matching primer as part of #552.
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@donkirkby
donkirkby committed May 13, 2020
1 parent 59399c6 commit 9453e44
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Showing 3 changed files with 76 additions and 61 deletions.
60 changes: 30 additions & 30 deletions micall/tests/microtest/2020A-GP41_S4_L001_R1_001.fastq
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Original file line number Diff line number Diff line change
@@ -1,40 +1,40 @@
@M01234:01:000000000-AAAAA:1:1101:02020:0001 1:N:0:4:starts_at_codon_2_and_inserts_extra_codon_after_codon_10
GTGGGAATAGGAGCTATGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACG
@M01234:01:000000000-AAAAA:1:1101:2020:0001 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0002 1:N:0:4
GTGGGAATAGGAGCTATGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0002 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0003 1:N:0:4
GTGGGAATAGGAGCTATGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0003 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0004 1:N:0:4
GTGGGAATAGGAGCTATGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0004 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0005 1:N:0:4
GTGGGAATAGGAGCTATGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0005 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0006 1:N:0:4
GTGGGAATAGGAGCTATGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0006 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0007 1:N:0:4
GTGGGAATAGGAGCTATGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0007 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0008 1:N:0:4
GTGGGAATAGGAGCTATGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0008 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0009 1:N:0:4
GTGGGAATAGGAGCTATGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0009 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0010 1:N:0:4
GTGGGAATAGGAGCTATGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0010 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
60 changes: 30 additions & 30 deletions micall/tests/microtest/2020A-GP41_S4_L001_R2_001.fastq
View file
Original file line number Diff line number Diff line change
@@ -1,40 +1,40 @@
@M01234:01:000000000-AAAAA:1:1101:02020:0001 2:N:0:4:starts_at_codon_2_and_inserts_extra_codon_after_codon_10
CGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACATAGCTCCTATTCCCAC
@M01234:01:000000000-AAAAA:1:1101:2020:0001 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0002 2:N:0:4
CGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACATAGCTCCTATTCCCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0002 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0003 2:N:0:4
CGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACATAGCTCCTATTCCCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0003 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0004 2:N:0:4
CGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACATAGCTCCTATTCCCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0004 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0005 2:N:0:4
CGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACATAGCTCCTATTCCCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0005 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0006 2:N:0:4
CGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACATAGCTCCTATTCCCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0006 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0007 2:N:0:4
CGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACATAGCTCCTATTCCCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0007 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0008 2:N:0:4
CGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACATAGCTCCTATTCCCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0008 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0009 2:N:0:4
CGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACATAGCTCCTATTCCCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0009 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:02020:0010 2:N:0:4
CGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACATAGCTCCTATTCCCAC
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0010 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17 changes: 16 additions & 1 deletion micall/tests/microtest/make_sample.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,22 @@ def main():
True,
(FastqSection('HIV1-CON-XX-Consensus-seed', 855, 906, 10),
FastqSection('HIV1-CON-XX-Consensus-seed', 912, 960, 10))),
FastqFile('2020A-GP41_S4_L001_R1_001.fastq',
'2020',
False,
(FastqSection('GP41',
2,
30,
10,
(CodonMutation(10, 'GGGATA'),)),)),
FastqFile('2020A-GP41_S4_L001_R2_001.fastq',
'2020',
True,
(FastqSection('GP41',
2,
30,
10,
(CodonMutation(10, 'GGGATA'),)),)),
FastqFile('2040A-HLA-B_S6_L001_R1_001.fastq',
'2040',
False,
Expand Down Expand Up @@ -175,7 +191,6 @@ def main():
'2190',
True,
(FastqSection('SARS-CoV-2-orf1ab', 4393, 4413, 100),))]
fastq_files = fastq_files[-2:]
for fastq_file in fastq_files:
with open(fastq_file.name, 'w') as f:
next_cluster = 1
Expand Down

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