[Biopython] BioPython unit tests: Samtools

[Fields, Christopher J]

We ran into a similar issue with the perl wrappers. IIRC the problem lay with some of the function definitions (mpileup being one) moving to htslib based on common usage in other packages like bcftools.  Should be much easier to deal with in Python than the fun that is Perl XS :)

chris

> On Sep 23, 2015, at 9:01 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 
> Hi Andreas,
> 
> Can you confirm which version of samtools is being used?
> 
> Many of the options changed from 0.1.19 to 1.3, and backward
> compatibility wasn't always preserved,  so my guess is this is a
> side effect.
> 
> Saket - are you interested in updating your original samtools
> wrappers?
> 
> Peter
> 
> On Wed, Sep 23, 2015 at 2:35 PM, Andreas Tille <andreas at an3as.eu> wrote:
>> [Bouncing my mails to Peter Cock since spam means rejected my mails,
>> sorry Peter, just let me know how to at best report bugs preferably
>> via mail]
>> 
>> Hi,
>> 
>> I try to activate all possible tests of BioPython at Debian package
>> build time but I found some issues.  I will discuss these in separate
>> mails, continuing with test_samtools_tool and python2.7:
>> 
>> ======================================================================
>> ERROR: test_mpileup_list (test_samtools_tool.SamtoolsTestCase)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>  File "/tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_samtools_tool.py", line 220, in test_mpileup_list
>>    stdout, stderr = cmdline()
>>  File "/tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Application/__init__.py", line 515, in __call__
>>    stdout_str, stderr_str)
>> ApplicationError: Non-zero return code 255 from 'samtools mpileup /tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/SamBam/bam1.bam /tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/SamBam/bam2.bam', message '[mpileup] 2 samples in 2 input files'
>> 
>> ======================================================================
>> FAIL: test_view (test_samtools_tool.SamtoolsTestCase)
>> Test for samtools view
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>  File "/tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_samtools_tool.py", line 123, in test_view
>>    % (cmdline, stderr_sam))
>> AssertionError: SAM file  viewing failed:
>> samtools view -S /tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/SamBam/sam1.sam
>> Stderr:
>> 
>> ----------------------------------------------------------------------
>> 
>> 
>> 
>> Unfortunately I have no idea how to deal with this.  Any hint?
>> 
>> Kind regards
>> 
>>        Andreas.
>> 
>> --
>> http://fam-tille.de
> 
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