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Build 2020A microtest sample from seed instead of gene as part of #552.
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@donkirkby
donkirkby committed May 14, 2020
1 parent 9453e44 commit 7b1626f
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Showing 4 changed files with 29 additions and 29 deletions.
20 changes: 10 additions & 10 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:1:1101:2020:0001 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
GTGGGAATAGGAGCTCTGTTCCTTGGGATATTCTTAGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0002 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
GTGGGAATAGGAGCTCTGTTCCTTGGGATATTCTTAGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0003 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
GTGGGAATAGGAGCTCTGTTCCTTGGGATATTCTTAGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0004 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
GTGGGAATAGGAGCTCTGTTCCTTGGGATATTCTTAGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0005 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
GTGGGAATAGGAGCTCTGTTCCTTGGGATATTCTTAGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0006 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
GTGGGAATAGGAGCTCTGTTCCTTGGGATATTCTTAGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0007 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
GTGGGAATAGGAGCTCTGTTCCTTGGGATATTCTTAGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0008 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
GTGGGAATAGGAGCTCTGTTCCTTGGGATATTCTTAGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0009 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
GTGGGAATAGGAGCTCTGTTCCTTGGGATATTCTTAGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0010 1:N:0:1
GTGGGAATAGGAGCTTTGTTCCTTGGGATATTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCC
GTGGGAATAGGAGCTCTGTTCCTTGGGATATTCTTAGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGGCC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20 changes: 10 additions & 10 deletions micall/tests/microtest/2020A-GP41_S4_L001_R2_001.fastq
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Original file line number Diff line number Diff line change
@@ -1,40 +1,40 @@
@M01234:01:000000000-AAAAA:1:1101:2020:0001 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
GGCCTGTACCGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCTAAGAATATCCCAAGGAACAGAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0002 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
GGCCTGTACCGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCTAAGAATATCCCAAGGAACAGAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0003 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
GGCCTGTACCGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCTAAGAATATCCCAAGGAACAGAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0004 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
GGCCTGTACCGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCTAAGAATATCCCAAGGAACAGAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0005 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
GGCCTGTACCGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCTAAGAATATCCCAAGGAACAGAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0006 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
GGCCTGTACCGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCTAAGAATATCCCAAGGAACAGAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0007 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
GGCCTGTACCGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCTAAGAATATCCCAAGGAACAGAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0008 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
GGCCTGTACCGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCTAAGAATATCCCAAGGAACAGAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0009 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
GGCCTGTACCGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCTAAGAATATCCCAAGGAACAGAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
@M01234:01:000000000-AAAAA:1:1101:2020:0010 2:N:0:1
GGCCTGTACCGTCAGCGTCATTGAGGCTGCGCCCATAGTGCTTCCTGCTGCTCCCAAGAATATCCCAAGGAACAAAGCTCCTATTCCCAC
GGCCTGTACCGTCAGCGTCATTGACGCTGCGCCCATAGTGCTTCCTGCTGCTCCTAAGAATATCCCAAGGAACAGAGCTCCTATTCCCAC
+
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16 changes: 8 additions & 8 deletions micall/tests/microtest/make_sample.py
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Original file line number Diff line number Diff line change
Expand Up @@ -64,19 +64,19 @@ def main():
FastqFile('2020A-GP41_S4_L001_R1_001.fastq',
'2020',
False,
(FastqSection('GP41',
2,
30,
(FastqSection('HIV1-B-FR-KF716496-seed',
6957,
7044,
10,
(CodonMutation(10, 'GGGATA'),)),)),
(CodonMutation(6981, 'GGGATA'),)),)),
FastqFile('2020A-GP41_S4_L001_R2_001.fastq',
'2020',
True,
(FastqSection('GP41',
2,
30,
(FastqSection('HIV1-B-FR-KF716496-seed',
6957,
7044,
10,
(CodonMutation(10, 'GGGATA'),)),)),
(CodonMutation(6981, 'GGGATA'),)),)),
FastqFile('2040A-HLA-B_S6_L001_R1_001.fastq',
'2040',
False,
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2 changes: 1 addition & 1 deletion release_test_microtest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,7 @@ def check_2020(self):
pos = int(row['refseq.nuc.pos'])
assert row['seed'] in expected_seeds, pos
assert row['region'] == 'GP41', pos
if 3 < pos <= 81:
if 3 < pos <= 90:
assert row['coverage'] == '10', pos
else:
assert row['coverage'] == '0', pos
Expand Down

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