[Bioperl-l] Bio::AlignIO error

[Jason Stajich]

done. thanks alex.

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

On Apr 12, 2005, at 4:53 AM, Alex Brown wrote:

> I believe I have found an error in Bio::AlignIO - I was getting 
> unrealistic results from $aln->no_residues. I traced this to the 
> no_residues subroutine in Bio::SimpleAlign:
>
> sub no_residues {
>     my $self = shift;
>     my $count = 0;
>
>     foreach my $seq ($self->each_seq) {
> 	my $str = $seq->seq();
>
> 	$count += ($str =~ s/[^A-Za-z]//g);
>     }
>
>     return $count;
> }
>
> I think line 8 of the subroutine should read:
>
> $count += ($str =~ s/[A-Za-z]//g);
>
> Cheers,
>
> Alex Brown.
>
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