[Biopython-dev] MAF Parser/Writer/Indexer

[Peter Cock]

On Fri, May 13, 2011 at 10:26 PM, Andrew Sczesnak wrote:
> Hi All,
>
> I'd like to contribute MAF parser/writer classes to Bio.AlignIO.  MAF is an
> alignment format used for whole genome alignments, as in the 30-way (or
> more) multiz alignments at UCSC:
>
> http://hgdownload.cse.ucsc.edu/goldenPath/mm9/multiz30way/maf/
>
> A description of the format is available here:
>
> http://genome.ucsc.edu/FAQ/FAQformat#format5
>

I've spoken to Andrew briefly before this, and I'm keen to get
the core functionality of parsing and writing MAF alignments
added to AlignIO. His other ideas for indexing these alignments
are much more interesting - and part of a more general topic
related to things like Ace alignments, or SAM/BAM alignments.
Ideally we can come up with something that will work for more
than just MAF alignments.

Peter