[Biopython-dev] Alignment object

[Kevin Jacobs <jacobs@bioinformed.com>]

On Tue, Mar 2, 2010 at 7:25 AM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Wed, Oct 28, 2009 at 12:18 PM, Brad Chapman <chapmanb at 50mail.com>
> wrote:My code does not (yet) attempt to deal with next-gen sequencing
> alignments, which would require padding all the (short) reads with
> leading and trailing gaps to ensure all rows of the alignment have
> the same length. Doing this in a memory efficient way could be
> done with a PaddedSeq object, or a very different alignment object
> (hold read and their offsets in memory). I'm not sure what is best,
> but the bx-python model looks worth understanding to help decide.
>
> Perhaps until this is settled, it would be premature to merge my
> alignment class to the trunk. After all, we may need to tweak the
> alignment object class heirachy.


Hi Peter,

I'm just jumping in here and have not yet read all of the background
material.  However, I am working with next-gen alignments and am curious as
to what you have in mind.  At first glance, it sounds like you want to
access aligned reads in a 'pileup' format (i.e., an object model akin to
http://samtools.sourceforge.net/pileup.shtml).  Or are you thinking of
something different entirely?

Best regards,
-Kevin