[Bioperl-l] want score from needle output

Chris Fields cjfields at uiuc.edu
Wed Jan 31 09:21:54 EST 2007


On Jan 31, 2007, at 4:25 AM, neeti somaiya wrote:

> Hi,
>
> I am using a code like the following to parse needle output. While  
> I am able
> to get the percent identity value, the score method is not returning
> anything, though the needle output does report a score too.
>
> --------------------------------
> my $str = Bio::AlignIO->new(-format => 'emboss',-file =>  
> $needle_output);
> my $aln = $str->next_aln();
>
> my $aln_perc_iden = $aln->percentage_identity;
> my $aln_score = $aln->score;
> -----------------------------
>
> Can anyone suggest what the problem could be?
>
> -- 
> -Neeti
> Even my blood says, B positive
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It's possible the needle output has changed.  What version of EMBOSS  
are you using?

chris



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