[Biopython-dev] XMFA format support

[Nick Loman]

On 26/01/2011 14:32, Peter Cock wrote:
>> 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.
> 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.
Hi Peter,

Sure, I'll have a go at writing a parser and let you know how I get on.

> 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.
>
I think the format was invented by the author of LAGAN 
(http://lagan.stanford.edu/lagan_web/index.shtml). From a Google search 
it looks like it is exported by Bigsdb too 
(http://pubmlst.org/software/database/bigsdb/userguide/isolates/xmfa.shtml)

Cheers

Nick