[Biopython-dev] samtools threaded daemon

[Saket Choudhary]

Just completed writing samtools wrapper :
https://github.com/biopython/biopython/pull/180

Unit Tests pending.

On 11 April 2013 23:51, Chris Mitchell <chris.mit7 at gmail.com> wrote:
> Here's the branch I'm starting with, including a working mpileup daemon for
> those who want to use it:
>
> https://github.com/chrismit/biopython/tree/samtools
>
> sample usage:
> from Bio.SamTools import SamTools
> sTools = '/home/chris/bin/samtools'
> hg19 = '/media/chris/ChrisSSD/ref/human/hg19.fa'
> bamSource = '/media/chris/ChrisSSD/TH1Alignment/NK/accepted_hits.bam'
> st = SamTools(bamSource,binary=sTools,threads=30)
>
> #now with a callback, which is advisable to use to process data as it is
> generated
> def processPileup(pileup):
>     print 'to process',pileup
>
> #st.mpileup(f=hg19,r=['chr1:%d-%d'%(i,i+1) for i in
> xrange(2000001,2001001)],callback=processPileup) #with callback
> #print st.mpileup(f=hg19,r=['chr1:%d-%d'%(i,i+1) for i in
> xrange(2000001,2000101)]) #will just return as a list
>
>
> On Thu, Apr 11, 2013 at 10:04 AM, Chris Mitchell <chris.mit7 at gmail.com>wrote:
>
>> Given that we'd be chasing after the samtools development cycle, I think
>> it's just easier to implement command line wrappers that are dynamic enough
>> to handle future versions.  For instance, some of the code doesn't seem too
>> set in stone and appears empirical (the BAQ computation comes to mind) and
>> therefore probable to change in future versions.  I can package in my
>> existing pileup parser, but in general I think most people will be using a
>> callback routine to handle it themselves since use cases of the final
>> output sort of vary project by project.
>>
>> Chris
>>
>>
>> On Thu, Apr 11, 2013 at 9:54 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:
>>
>>> On Thu, Apr 11, 2013 at 2:46 PM, Chris Mitchell <chris.mit7 at gmail.com>
>>> wrote:
>>> > Also, if a binary can't be found, having it fallback to the future
>>> > BioPython parser seems like it might be a good idea (provided it has
>>> > similar functionality like creating pileups, does it?).
>>>
>>> It has the low level random access via the BAI index done, but
>>> does not yet have a reimplementation of the mpileup code, no.
>>> (Would that be useful compared to calling samtools and parsing
>>> its output?)
>>>
>>> Peter
>>>
>>
>>
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