[Biopython-dev] samtools threaded daemon

[Peter Cock]

On Thu, Apr 11, 2013 at 7:10 AM, Christian Brueffer
<christian at brueffer.de> wrote:
> On 4/11/13 4:57 , Chris Mitchell wrote:
>> Hi everyone,
>>
>> I've been doing a ton of mpileup work recently with samtools so I made a
>> python daemon to parallelize the process.  Is there any interest in a
>> generic SamTools package for BioPython?  I know pysam exists, but it'd be
>> an added dependency as well as not threaded.  In my experience, for
>> querying a ton of positions threading mpileup is the best way to go (much
>> faster than -l bed_file in my use cases).  If there's interest, I'll
>> package it as a general SamTools command line wrapper with the added
>> bonuses that for certain operations you can input a list and thread those
>> parts.
>>
>
> Hi Chris,
>
> sounds great!  I use samtools/pysam a lot, so I'd appreciate another
> option.  My collegue uses mpileup with pysam a lot as well, I'm sure he
> wouldn't mind some speedup in that area.
>
> Cheers,
>
> Chris

A samtools command line wrapper sounds useful in itself. Saket has
done a bwa wrapper I need to merge:
https://github.com/biopython/biopython/pull/167

I think he was planning to do samtools next:
https://github.com/saketkc/biopython/tree/samtools_wrapper

What did you have in mind for threading? Automatically calling
multiple independent samtools processes in the background?

Peter

P.S. See also this thread:
http://lists.open-bio.org/pipermail/biopython-dev/2013-April/010492.html