[Bioperl-l] Re: Bio::SearchIO::amps and Bio::SearchIO::mrbayes_nexus

[Matthew Betts]

Sorry, meant Bio::AlignIO::*

(oops)

On Wed, 11 May 2005, Matthew Betts wrote:

>
> Hi,
>
> I was thinking of writing a Bio::SearchIO module for AMPS block format. This 
> is the format used by alscript and stamp. Both of these come with format 
> converters, but would be useful for me to do it within bioperl. OK for me to 
> write Bio::SearchIO::amps, or is there something else already? Is that name 
> OK?
>
> Secondly, MrBayes doesn't like some things in the Nexus format output by 
> Bio::SearchIO::nexus (the 'symbols' parameter, and it expects 'end;' rather 
> than 'endblock;') even though they're valid nexus... OK to copy 
> Bio::SearchIO::nexus to Bio::SearchIO::mrbayes_nexus and make the necessary 
> changes, or is there a better way? (Though a full nexus parser and flexible 
> outputter looks like a nightmare...)
>
> Thanks,
>
> Matthew
>
>

-- 
Matthew Betts, Post Doc, Computational Biology Unit,
BCCS, HiB, UiB, Thormøhlensgt. 55, 5008 Bergen, Norway
tlf: (+47) 55 58 40 22, fax: (+47) 55 58 42 95
mailto:matthew.betts at bccs.uib.no, www.ii.uib.no/~matthewb