[Biopython] subprocess.Popen problem

[Peter Cock]

On Wed, Nov 2, 2011 at 4:39 AM, Mic <mictadlo at gmail.com> wrote:
> Hello,
> I have tried to write a SOAPaligner wrapper in oder to get the SOAP
> alignment statistics:
>
> Total Pairs: 1000 PE
> Paired:      35 ( 3.50%) PE
> Singled:     170 ( 8.50%) SE
> Total Elapsed Time:           24.00
>      - Load Index Table:     23.22
>      - Alignment:             0.78
>
> with the following code:
>
> import os, subprocess
> if __name__ == '__main__':
>    try:
>        cmd_soap = 'soap -p 1 -a test_A_clonesremoved-tiny.fastq -b
> test_B_clonesremoved-tiny.fastq -D all.m.fasta.index -r 0 -o
> test_clonesremoved-tiny_vs_all.m.paired.soap -2
> test_clonesremoved-tiny_vs_all.m.single.soap -m 100 -x 550'
>        proc = subprocess.Popen(cmd_soap, shell=True)
>        returncode = proc.wait()
>        print returncode
>    except Exception, e:
>        sys.stderr.write( "%s\n" % str(e))
>        sys.exit()
>
>
> However, when I started the script I just got 0 as an output:
>
> $ python soap_wrapper.py
>
> Begin Program SOAPaligner/soap2
> Wed Nov  2 14:23:33 2011
> Reference: all.m.fasta.index
> Query File a: test_A_clonesremoved-tiny.fastq
> Query File b: test_B_clonesremoved-tiny.fastq
> Output File: test_clonesremoved-tiny_vs_all.m.paired.soap
>             test_clonesremoved-tiny_vs_all.m.single.soap
> Load Index Table ...
> Load Index Table OK
> Begin Alignment ...
> 2000 ok    0.76 sec
> Total Pairs: 1000 PE
> Paired:      35 ( 3.50%) PE
> Singled:     170 ( 8.50%) SE
> Total Elapsed Time:           24.00
>      - Load Index Table:     23.22
>      - Alignment:             0.78
>
> SOAPaligner/soap2 End
> Wed Nov  2 14:23:57 2011
>
> 0
>
> What did I wrong?
>
> Thank you in advance.
>

Command line tools typically return 0 for success, anything else
is usually an error code. You can double check the return code
from the command line outside Python - e.g. a quick shell script
to call the command and echo the return code to the terminal.

Peter