[BioRuby] Clustal ALN writer

[Naohisa GOTO]

Hi Pjotr,

There is already Bio::Alignment#output_clustal method.
It is implemented in Bio::Alignment::Output module.

http://bioruby.org/rdoc/classes/Bio/Alignment/Output.html#M000092

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Tue, 5 Jan 2010 13:39:02 +0100
Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> I propose to write an ALN output writer. ALN files show aligned
> sequences with additional lines of information (like a match line). I
> want to use it to output PAML positive selection sites. This is
> the idea:
> 
> 
> SEQ1  alignment 1...
> SEQ2  alignment 2...
>       ...*.:*....***  (match line)
>       ...*....*.....  (pos. sel. line)
> 
> Do we want such ALN output (I think it is allowed), and can we allow
> for the additional output. I have a proposed interface here:
>  
>   http://github.com/pjotrp/bioruby/commit/7f320781039b56aee991ab72404655fae210e2cb
> 
> I notice ClustalW.to_fasta has been obsoleted. But we don't have
> to_aln yet, and we need to allow adding match_lines and other
> information.
> 
> Pj.
>