[Bioperl-l] Getting score from Emboss-type alignment (water)

[Jason Stajich]

Scores are set by the Alignment parser - we separate the 'running' from 
the 'parsing'.
Bio::AlignIO::emboss had to be updated.

-jason
On Dec 13, 2004, at 5:56 AM, Pawel Szczesny wrote:

> Hello,
>
> I have a problem in extracting score from alignment in EMBOSS format 
> (water in this case).
>
> The code:
>
> my $in = new Bio::AlignIO(-format => 'emboss',-file   => 'test.water');
> while( my $aln = $in->next_aln ) {
>                print $aln->score;
>           }
>
> $aln->score seems to be undefined. File emboss.pm from BioPerl Live 
> has additional lines compared to stable distribution, but I have no 
> idea why even with patching emboss.pm it doesn't work at all.
>
> Any ideas? I was searching documentation, but reporting score seem to 
> be implemented only in Blast parser.
>
> Regards
> Pawel Szczesny
>
>
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/