[Bioperl-l] rev translating stop codons with Bio::Tools::CodonTable

[Heikki Lehvaslaiho]

Jamie,

You are right. That fixes that problem. I'll se that this gets fixed
properly.

	-Heikki

On Wed, 2002-10-30 at 23:44, Jamie Hatfield wrote:
> I'm new to Bioperl myself, but after looking through the source for
> Bio::SeqUtils->valid_aa (which Bio::Tools::CodonTable uses to generate
> its $VALID_PROTEIN list), the following code seems to be suspect...
> 
> sub valid_aa {
>    my ($self,$code) = @_;
> 
>    if( ! $code ) { 
>        my @codes;
>        foreach my $c ( sort values %ONECODE ) {
> 	   push @codes, $c unless ( $c =~ /[BZX\*]/ );
>        }
>        push @codes, qw(B Z X); # so they are in correct order ?
> return @codes;
>   } 
>   :
>   :
>   :
> }
> 
> We don't push on codes B, Z, X, or *, and then we put B, Z, and X on at
> the end.  '*' will never be pushed on, and therefore, the check in
> Bio::Tools::CodonTable->revtranslate 
> 
> if ( defined $value and $value =~ /$VALID_PROTEIN/ ...
> 
> Will fail for '*'.
> 
> 
> > -----Original Message-----
> > From: bioperl-l-admin@bioperl.org 
> > [mailto:bioperl-l-admin@bioperl.org] On Behalf Of David Messina
> > Sent: Wednesday, October 30, 2002 4:04 PM
> > To: bioperl-l@bioperl.org
> > Subject: [Bioperl-l] rev translating stop codons with 
> > Bio::Tools::CodonTable
> > 
> > 
> > Hi all,
> > 
> > I looked in the email archive, and I couldn't find any mention of a 
> > similar problem. Would you please take a moment to examine the 
> > following?
> > 
> > I can't get Bio::Tools::CodonTable to reverse translate stop 
> > symbols (* 
> > or Ter) to codons (TAA, TAG, TGA). It works fine in the other 
> > direction, translating TAA, TAG, and TGA to *.
> > 
> > Please see the sample code and its output:
> > 
> > #!/usr/local/bin/perl -w
> > 
> > use Bio::Tools::CodonTable;
> > $myCodonTable = Bio::Tools::CodonTable->new();
> > 
> > # This loop tests rev translation of stops.
> > # I've put just A and C for this example, but I've tested all 20 
> > standard amino acids.
> > foreach my $aa ('A', 'C', 'Ter', '*')
> > {
> >      my @codons = $myCodonTable->revtranslate($aa);
> >      if (! @codons) { print "WARNING: no codons for $aa!\n"; }
> > 
> >          foreach my $codon (@codons)
> >          {
> >              print $aa, " ", $codon, "\n";
> >          }
> > }
> > 
> > # This loop tests regular forward translation of stops.
> > foreach my $codon ('TAA', 'TAG', 'TGA')
> > {
> >      print $codon, " ", $myCodonTable->translate($codon), "\n";
> > }
> > 
> > PROGRAM OUTPUT
> > ----------------------------
> > A gct
> > A gcc
> > A gca
> > A gcg
> > C tgt
> > C tgc
> > WARNING: no codons for Ter!
> > WARNING: no codons for *!
> > TAA *
> > TAG *
> > TGA *
> > 
> > I am running BioPerl 1.0.2 with Perl 5.8.0 under Mac OS X 
> > 10.1.2. Your 
> > help is greatly appreciated.
> > 
> > 
> > David Messina
> >    Division of Human Genetics
> >    Washington Univ. in St. Louis
> >    dmessina@genetics.wustl.edu
> >    314/747-1063 fx 314/747-2489
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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