diff --git a/micall/tests/microtest/2020A-GP41_S4_L001_R1_001.fastq b/micall/tests/microtest/2020A-GP41_S4_L001_R1_001.fastq index e6929b96d..43962a9af 100644 --- a/micall/tests/microtest/2020A-GP41_S4_L001_R1_001.fastq +++ b/micall/tests/microtest/2020A-GP41_S4_L001_R1_001.fastq @@ -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 diff --git a/micall/tests/microtest/2020A-GP41_S4_L001_R2_001.fastq b/micall/tests/microtest/2020A-GP41_S4_L001_R2_001.fastq index 95ebe813a..c593705af 100644 --- a/micall/tests/microtest/2020A-GP41_S4_L001_R2_001.fastq +++ b/micall/tests/microtest/2020A-GP41_S4_L001_R2_001.fastq @@ -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 diff --git a/micall/tests/microtest/make_sample.py b/micall/tests/microtest/make_sample.py index e4105deff..2604bc778 100644 --- a/micall/tests/microtest/make_sample.py +++ b/micall/tests/microtest/make_sample.py @@ -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, diff --git a/release_test_microtest.py b/release_test_microtest.py index dd375b79e..cfdc10cba 100644 --- a/release_test_microtest.py +++ b/release_test_microtest.py @@ -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