Control: tags -1 - pending Hi, removing the pending tag, as there are still some test failures which seem related to bowtie2 this time. Given the output, results look off by two. I don't know for sure if this is significant or might just need refresh as well. See below:
_________________________ TestMapping.test_run_bowtie2
_________________________
self = <ariba.tests.mapping_test.TestMapping
testMethod=test_run_bowtie2>
def test_run_bowtie2(self):
'''Test run_bowtie2 unsorted'''
self.maxDiff = None
ref = os.path.join(data_dir, 'mapping_test_bowtie2_ref.fa')
reads1 = os.path.join(data_dir,
'mapping_test_bowtie2_reads_1.fq')
reads2 = os.path.join(data_dir,
'mapping_test_bowtie2_reads_2.fq')
out_prefix = 'tmp.out.bowtie2'
mapping.run_bowtie2(
reads1,
reads2,
ref,
out_prefix,
bowtie2=extern_progs.exe('bowtie2'),
bowtie2_version=extern_progs.version('bowtie2'),
)
expected = get_sam_columns(os.path.join(data_dir,
'mapping_test_bowtie2_unsorted.bam'))
got = get_sam_columns(out_prefix + '.bam')
> self.assertListEqual(expected, got)
E AssertionError: Lists differ: [('1'[508 chars]5', 99, 'ref', 0,
[(4, 2), (0, 23)], 'CCTCCACA[346 chars]AT')] != [('1'[508 chars]5', 97, 'ref',
0, [(4, 2), (0, 23)], 'CCTCCACA[346 chars]AT')]
E
E First differing element 8:
E ('5', 99, 'ref', 0, [(4, 2), (0, 23)],
'CCTCCACAGGATGGTGGTATACCTG')
E ('5', 97, 'ref', 0, [(4, 2), (0, 23)],
'CCTCCACAGGATGGTGGTATACCTG')
E
E [('1', 99, 'ref', 0, [(4, 5), (0, 20)],
'AGCCCTCCACAGGATGGTGGTATAC'),
E ('1', 147, 'ref', 30, [(0, 25)],
'AGGATACAGATCTTGTGGGAAAGGT'),
E ('2', 99, 'ref', 124, [(0, 25)],
'TAATGTTCTTAGGGCTTACCATAGA'),
E ('2', 147, 'ref', 170, [(0, 20), (4, 5)],
'TCCACCTTAGCTAAGCGCAGACTCG'),
E ('3', 73, 'ref', 86, [(0, 25)], 'TCGGGTCTGTACAAGGACGGATGGT'),
E ('3', 133, None, 86, [], 'CGTACTGACTGACTGACGTACTGCA'),
E ('4', 99, 'ref', 55, [(0, 25)], 'CCGCCGGGAAGTCCTTCTGTCGTGC'),
E ('4', 147, 'ref', 136, [(0, 25)],
'GGCTTACCATAGAGGTACACTAAAA'),
E - ('5', 99, 'ref', 0, [(4, 2), (0, 23)],
'CCTCCACAGGATGGTGGTATACCTG'),
E ? ^
E
E + ('5', 97, 'ref', 0, [(4, 2), (0, 23)],
'CCTCCACAGGATGGTGGTATACCTG'),
E ? ^
E
E - ('5', 147, 'ref', 166, [(0, 24), (4, 1)],
'TTCATCCACCTTAGCTAAGCGCAGA'),
E ? ^
E
E + ('5', 145, 'ref', 166, [(0, 24), (4, 1)],
'TTCATCCACCTTAGCTAAGCGCAGA'),
E ? ^
E
E ('6', 77, None, -1, [], 'CAGTTGCATGACGTCATGCAGTCAT'),
E ('6', 141, None, -1, [], 'AATGAGTATGATGAGTAATGGTATG'),
E - ('7', 99, 'ref', 56, [(4, 1), (0, 23), (4, 1)],
'ACGCCGGGAAGTCCTTCTGTCGTGT'),
E ? ^
E
E + ('7', 97, 'ref', 56, [(4, 1), (0, 23), (4, 1)],
'ACGCCGGGAAGTCCTTCTGTCGTGT'),
E ? ^
E
E - ('7', 147, 'ref', 136, [(0, 24), (4, 1)],
'GGCTTACCATAGAGGTACACTAAAT')]
E ? ^
E
E + ('7', 145, 'ref', 136, [(0, 24), (4, 1)],
'GGCTTACCATAGAGGTACACTAAAT')]
E ? ^
ariba/tests/mapping_test.py:62: AssertionError
----------------------------- Captured stderr call
-----------------------------
[E::idx_find_and_load] Could not retrieve index file for
'/builds/med-team/ariba/debian/output/source_dir/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_bowtie2_unsorted.bam'
[E::idx_find_and_load] Could not retrieve index file for
'tmp.out.bowtie2.bam'
____________________ TestMapping.test_run_bowtie2_and_sort
_____________________
self = <ariba.tests.mapping_test.TestMapping
testMethod=test_run_bowtie2_and_sort>
def test_run_bowtie2_and_sort(self):
'''Test run_bowtie2 sorted'''
ref = os.path.join(data_dir, 'mapping_test_bowtie2_ref.fa')
reads1 = os.path.join(data_dir,
'mapping_test_bowtie2_reads_1.fq')
reads2 = os.path.join(data_dir,
'mapping_test_bowtie2_reads_2.fq')
out_prefix = 'tmp.out.bowtie2'
mapping.run_bowtie2(
reads1,
reads2,
ref,
out_prefix,
sort=True,
bowtie2=extern_progs.exe('bowtie2'),
bowtie2_version=extern_progs.version('bowtie2'),
)
expected = get_sam_columns(os.path.join(data_dir,
'mapping_test_bowtie2_sorted.bam'))
got = get_sam_columns(out_prefix + '.bam')
> self.assertListEqual(expected, got)
E AssertionError: Lists differ: [('1'[67 chars]5', 99, 'ref', 0,
[(4, 2), (0, 23)], 'CCTCCACA[787 chars]TG')] != [('1'[67 chars]5', 97, 'ref',
0, [(4, 2), (0, 23)], 'CCTCCACA[787 chars]TG')]
E
E First differing element 1:
E ('5', 99, 'ref', 0, [(4, 2), (0, 23)],
'CCTCCACAGGATGGTGGTATACCTG')
E ('5', 97, 'ref', 0, [(4, 2), (0, 23)],
'CCTCCACAGGATGGTGGTATACCTG')
E
E Diff is 1363 characters long. Set self.maxDiff to None to see
it.
ariba/tests/mapping_test.py:105: AssertionError
----------------------------- Captured stderr call
-----------------------------
[E::idx_find_and_load] Could not retrieve index file for
'/builds/med-team/ariba/debian/output/source_dir/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_bowtie2_sorted.bam'
It wouldn't be the first time a library updates index of its
entries. Unless someone seems something wrong, I might just go
ahead and ajust the test suite accordingly.
Also, the package does not operate with python3.11 for now,
moving to default python only is still to do.
In hope this helps,
--
Étienne Mollier <emoll...@emlwks999.eu>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/3, please excuse my verbosity.
On air: Ayreon - 2084
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