[Biopython] BioPython unit tests: Samtools

[Saket Choudhary]

On 23 September 2015 at 07:01, 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?
>

Sure, I will try to send a PR later this week.


> 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