[Biopython-dev] XMFA format support

Peter Cock p.j.a.cock at googlemail.com
Wed Jan 26 14:32:41 UTC 2011

Hi Nick,

On Wed, Jan 26, 2011 at 2:23 PM, Nick Loman <n.j.loman at bham.ac.uk> wrote:
> Hi biopython-developers,
> Has anyone made a start on adding XMFA support to Bio.AlignIO?
> XMFA files are produced by software such as Mauve (amongst others).
> Here's an example file:
> http://www.bioperl.org/wiki/XMFA_multiple_alignment_format
> It should be relatively straight-forward to parse them in a basic way in
> that they can be split on the '=' line to produce the equivalent of
> multi-FASTA alignments.
> Cheers,
> Nick.

Nope, but you are right they should be easy to parse - especially
if you ignore the loosely defined optional key/value entries on the
equals line. Do you want to tackle this? If not, can you at least
provide some small example files and help with testing? You
could file an enhancement bug on our bugzilla and then upload
them as attachments.

Also, could you name any other software that outputs these XMFA
(extended multiple fasta) files, other than Mauve? I've not ever
come across this format before.



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