[Biopython] [Bio-bwa-help] making a "libbwa"

[Mic]

+1
BioRuby did it in the following way:

https://github.com/fstrozzi/bioruby-bwa/blob/master/ext/mkrf_conf.rb
https://github.com/fstrozzi/bioruby-bwa/wiki

Maybe it could be integrated to be Biopython?

Cheers,

On Thu, Mar 15, 2012 at 8:56 PM, Luca Pireddu <pireddu at crs4.it> wrote:

> Hello list,
>
> I'd like the discuss the idea of refactoring BWA to separate the
> alignment logic from the rest of the code base, thus resulting in a
> libbwa alignment library which could be used through the regular command
> line interface or through other means, as one saw fit.
>
> I'm one of the developers of Seal (http://biodoop-seal.sf.net/), a suite
> of Hadoop-based tools for the processing of sequencing data.  Within the
> Seal suite, we have the Seqal program for read mapping which at this
> time contains a "fork" of the BWA 0.5.10 code which we've patched in a
> few points and then built as a library that we can use within our
> application.  In this way, we can feed the alignment algorithm with read
> data we have pre-loaded in memory instead of files in a supported
> format, and we can also fetch the alignment results directory from BWA's
> memory structures rather than the regular output files.  The resulting
> library, as long as it has a stable API, provides much more flexibility
> than a command-line program, allowing it to be used more easily and
> elegantly in settings different from the regular fastq to sam/bam
> workflow/application.  Seqal is a concrete example.  As another example,
> we've built a Python interface for the library allowing us to easily use
> it in scripts and testing.
>
> If there is interest for this idea, especially on the part of Heng, we
> could discuss a viable API.  Myself and my colleagues are certainly
> willing to propose a first draft and even contribute the patches
> necessary to implement it.
>
> Looking forward to hearing from you,
>
> --
> Luca Pireddu
> CRS4 - Distributed Computing Group
> Loc. Pixina Manna Edificio 1
> 09010 Pula (CA), Italy
> Tel: +39 0709250452
>
>
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