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

[Chris Fields]

On May 28, 2009, at 4:27 PM, Tristan Lefebure wrote:

> 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*
> ---------------------------------------------------
>
> ...
>
> 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?

This is a bug within Bio::AlignIO::fasta and not LocatableSeq.  I just  
committed a fix for it to bioperl-live.

Just to note, this error message actually was present in all versions  
of bioperl with LocatableSeq.  However, there was a silent logic bug  
that prevented it from working up 'til 1.6.

> (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!

np.  thanks for finding the bug!

chris