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

Pawel Szczesny pawel.szczesny at tuebingen.mpg.de
Mon Dec 13 05:56:43 EST 2004


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.

Pawel Szczesny

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