[Biopython-dev] [Bug 2905] Short read alignment format SAM / BAM

[Kevin Jacobs <jacobs@bioinformed.com>]

On Thu, Jul 15, 2010 at 1:20 PM, Vince S. Buffalo <vsbuffalo at gmail.com>wrote:

> Sorry to bump this old topic, but are there plans to merge this into the
> main project? I do a lot of processing with the SAM format and it would be
> great to use Biopython for this.
>
> Does the pure Python implementation run as quickly as the pysam version? Is
> anyone still considering forking pysam and rewriting the C wrappers?
>
>
I also started writing a pure Python SAM/BAM reader/writer with Cython
accelerators, but quickly got distracted by the gaps in the "standard" and
quirks in the various implementations.  Instead, I've improved the base
pysam implementation, fixed the parts that weren't working for me, and have
posted a clone on the Google code site:

http://code.google.com/r/bioinformed-pysam/

Of course, this doesn't help with how best to add functionality to
BioPython...

-Kevin