[Biopython-dev] BWA Wrapper

[Kevin Jacobs]

FYI, I am working on a direct Cython wrapper around the new BWA-MEM
aligner, which will allow API-level access to Heng Li's extremely
impressive new algorithm.  It is still in early development and is missing
many bells and whistles, but will be shaping up in the next few weeks.

Test program:

import bwamem

mem = bwamem.MEMAligner('ref/human_g1k_v37.fasta')
a = mem.align('TCACGACGCTCTTCCGATCTGTT...GTGCATTCTCTGGTCAGACAGCCAAGG')
a = a[0]

print 'ref id =',a.rid
print 'pos    =',a.pos
print 'CIGAR  =',a.cigar.to_string()


Output (correct):

ref id = 0
pos    = 115250385
CIGAR  = 17N134M



On Wed, Mar 13, 2013 at 2:16 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Monday, March 4, 2013, Saket Choudhary wrote:
>
> > Hi,
> >
> > I have updated the code here :
> > https://github.com/saketkc/biopython/tree/bwa_wrapper
> >
> > I have added unittests for the wrapper. And yes, this did help me in
> > fixing a lot of minor bugs in my original wrapper.
> >
> > @Peter :  Is this 'pull request' ready ?
> >
> > Thanks
> >
> > Saket
> >
> >
> Sorry I've not had time to test this yet - and have
> been off ill today as well. The basic approach you've
> taken seems sound, and a good basis for other
> samtools style tools.
>
> Peter
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