[Biopython-dev] XMFA format support

Peter Cock p.j.a.cock at googlemail.com
Wed Jan 26 15:06:00 UTC 2011

On Wed, Jan 26, 2011 at 2:46 PM, Nick Loman <n.j.loman at bham.ac.uk> wrote:
> 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).
>>> ...
>> 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.

Great. I'd suggest format name "xmfa" to match BioPerl, and using
Bio/SeqIO/XmfaIO.py for your parser (and writer if you do one).


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