[Bioperl-l] BioAlignIO, protein sequences and stop codons

[Tristan Lefebure]

Hello,

This might be a new behavior since BioPerl1.6, but when I 
import protein alignments that contain STOP residues (i.e. 
*), I get the following warnings:


--------------------- WARNING ---------------------
MSG: In sequence tax1 residue count gives end value 5.  
Overriding value [4] with value 5 for 
Bio::LocatableSeq::end().
LSYC*
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: In sequence tax2 residue count gives end value 4.
Overriding value [3] with value 4 for 
Bio::LocatableSeq::end().
LY-F*
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: In sequence tax3 residue count gives end value 5.
Overriding value [4] with value 5 for 
Bio::LocatableSeq::end().
LSEW*
---------------------------------------------------

Is that something I should worry about? I guess this comes 
from the fact that range->end() does not count the STOP as 
residue, but why not? Alternatively how can I turn off the 
warning?

(And yes I want to keep the STOP codons, because I will use 
this amino-acid alignment with 
Bio::Align::Utilities::aa_to_dna_aln, and I don't want to 
loose the stop codon).

I attach a small example and data set bellow.

Thanks!

Script:
-----
#! /usr/bin/perl

use strict;
use warnings;
use Bio::AlignIO;


my $in = Bio::AlignIO->new(-file => "test2_aa.fas", -format 
=> 'fasta' );

my $aln = $in->next_aln();

----------


data: test2_aa.fas
----
>tax1
LSYC*
>tax2
LY-F*
>tax3
LSEW*
----