[Biopython-dev] Alignment object

[Kevin Jacobs <jacobs@bioinformed.com>]

On Thu, Mar 4, 2010 at 8:13 AM, Brad Chapman <chapmanb at 50mail.com> wrote:

> All of my work converts SAM directly into sorted and indexed BAM,
> and then build from that. For me, direct SAM parsing wouldn't be as
> useful as BAM.


Same here-- I construct and unserialize alignment data into SAM-like
records, but it would be foolish to actually store them natively to disk.


>
> > 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.
>
> Cool. Does the BAM reader require samtools C code or is it
> independent of that?
>

It is intended to be independent of the samtools distribution, though some
of the C code is currently duplicated (e.g., bgzf).  Of course, a
Cython/Python re-write would be simple enough, though obviously extra work.

-Kevin