[Bioperl-l] stockholm AlignIO write_aln method

[Jason Stajich]

Albert

write_aln should take a list of  Bio::Align::AlignI objects (more 
concretely, a Bio::SimpleAlign objects) and write them out using 
$self->_print.
AlignIO::clustalw is a good example.

Stockholm format is documented here:
http://www.cgb.ki.se/cgb/groups/sonnhammer/Stockholm.html

We don't really support the notion of #=GF, #=GC, #=GS, #=GR lines in 
Bioperl at this point although that would be nice so we can store and 
manipulate data like secondary structure strings within Bioperl.  I 
know some people had talked about this a long time ago, I don't think 
anything was done...

-jason
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/

On Mar 10, 2005, at 8:08 AM, Albert Vilella wrote:

> Hi,
>
> I'm willing to use the unimplemented write_aln method in stockholm
> format.
>
> As it isn't implemented, I would like to ask where could I find the doc
> files for the format and the minimal the set of rules write_aln method
> should obey,
>
> Anyone?
>
> Bests,
>
>     Albert.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
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