[Biopython] samtools does not return correct exit code

[Mic]

Thank you, pysam has similar problems and I posted already a bug report.
http://code.google.com/p/pysam/issues/detail?id=89
http://code.google.com/p/pysam/issues/detail?id=90

I am going to post on samtools mailing list the problem.

Cheers,


On Thu, Mar 1, 2012 at 9:00 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Thu, Mar 1, 2012 at 1:40 AM, Mic <mictadlo at gmail.com> wrote:
> > Hallo,
> > Samtools does not return correct the exit code:
> >
> > import subprocess
> > import logging
> > import sys
> >
> > def run_cmd(args):
> >        if subprocess.call(args,shell=True) != 0:
> >                print 'hello'
> >                logging.error("Error copying sequence file args='%s'" %
> > str(args))
> >                return 1
> >        print 'e', sys.stderr
> >        print 'o', sys.stdout
> >        return 0
> >
> >
> > def runSamtools( cmd ):
> >    '''run a samtools command'''
> >
> >    try:
> >        retcode = subprocess.call(cmd, shell=True)
> >        print retcode
> >        if retcode < 0:
> >            print >>sys.stderr, "Child was terminated by signal", -retcode
> >    except OSError, e:
> >        print >>sys.stderr, "Execution failed:", e
> >
> > print run_cmd("samtools faidx ex1.fa")
> > print runSamtools("samtools faidx ex1.fa")
> >
> > print 'Hello still alive'
> >
> >
> > and as output I got:
> >
> > $ python p3.py
> > open: No such file or directory
> > [_razf_open] fail to open ex1.fa
> > [fai_build] fail to open the FASTA file ex1.fa
> > e <open file '<stderr>', mode 'w' at 0x7ffa4658d270>
> > o <open file '<stdout>', mode 'w' at 0x7ffa4658d1e0>
> > 0
> > open: No such file or directory
> > [_razf_open] fail to open ex1.fa
> > [fai_build] fail to open the FASTA file ex1.fa
> > 0
> > None
> > Hello still alive
> >
> > How can I get sure that all samtools commands were executed successfully?
> >
> > Thank you in advance.
>
> Hi Mic,
>
> General Bioinformatics with Python questions are fine on the Biopython
> mailing list, but I think this qurey might be better asked elsewhere.
>
> Are you saying the samtools binary returns an error code 0 (success)
> even when it fails? If so, that should be raised as a bug with samtools.
>
> Alternatively pysam has support built in for calling the samtools commands.
> I'm not sure exactly how that works internally (e.g. via subprocess or by
> a C API call), but ask on the pysam mailing list.
>
> Regards,
>
> Peter
>