[Debian-med-packaging] Bug#1021675: ariba status in the vcs

[Étienne Mollier]

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 <emollier at 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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