[Biopython-dev] Alignment object

[Kevin Jacobs <jacobs@bioinformed.com>]

On Wed, Mar 3, 2010 at 10:57 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> I agree that we should work towards supporting SAM (and perhaps
> also BAM) in Biopython, and other projects APIs can be very
> useful for inspiration or guidance.
>
>
Honestly, the SAM/BAM format specification is pretty dodgy.  Thankfully
between samtools and Picard source code, I've been able to work out most of
the tricky bits.  I'm glad to know that the R folks are also working on
this, since they're usually very good about generating clear documentation.



> I was aware of pysam but am concerned about the dependencies:
> pyrex 0.9.8 or later, python 2.6 or later, plus of course SAMtools
> itself - which may all be fine on Linux, but will likely be trouble for
> us on other platforms (especially Windows).
>
> Is anyone aware of any other SAM/BAM parser in Python?


Parsing SAM is pretty simple and I can certainly help with gluing it into
Biopython (with some help on the Biopython side, since I'm still a newb).
I'm about half-way to having a BAM reader and writer for my own purposes.
 I'm coding the time-critical parts in Cython with a fallback to pure
Python, so it may not be ideal for use in Biopython.

-Kevin