[Bioperl-l] Bio::Tools::SeqStats count_codons

[Heikki Lehvaslaiho]

Govind,

Not having your data files, I truncated your code down to essentials:

#=============================================
use Bio::Seq;
use Bio::Tools::SeqStats;

$tseq = "atcgatgctagcwgcatgcatgctagwctag";
#$tseq = "ATCGATGCTAGCWGCATGCATGCTAGWCTAG";

$codobj=Bio::Seq->new('-seq' => $tseq,
        '-alphabet' => 'dna'
        );
$ss=Bio::Tools::SeqStats->new(-seq => $codobj);
$refcount = $ss->count_codons();

foreach $codon (sort keys(%$refcount)) {
    print("$codon   $refcount->{$codon}\n");
}
#================================================


I understand that you get different results depending case. Try this with both 
$tseq values. I get a warning and same number of codons in both cases 
(ignoring the case). Do you?

 -Heikki

On Tuesday 27 September 2005 16:15, Govind Chandra wrote:
> The count_codons method in Bio::Tools::SeqStats seems to be case
> sensitive. See script below. Is this intended? Or am I doing something
> silly.
>
> ### script begin ###
> use Bio::SeqIO;
> use Bio::Seq;
> use Bio::Tools::SeqStats;
> $seqio=Bio::SeqIO->new('-file' => 'Ssc.fas',
>                        '-format' => 'fasta');
>
> $seqobj=$seqio->next_seq();
>
> open(ORFS, "<ordered_all_orfs.out");
>
> while(<ORFS>) {
> chomp();
> ($strand, $start, $end, $nt_len, $aa_len)=split(/\s+/, $_);
> #print("$strand   $start   $end   $nt_len   $aa_len\n");
>
> if($strand==1) {
> $cdsobj=$seqobj->trunc($start, $end);
> }
> elsif($strand==-1) {
> $cdsobj=$seqobj->trunc($start, $end)->revcom();
> }
>
> $tseq=uc($cdsobj->seq());  # works
> #$tseq=$cdsobj->seq(); # does not work. given and ambiguous count only
>
> $codobj=Bio::Seq->new('-seq' => $tseq,
>         '-alphabet' => 'dna'
>         );
>
> print(">$strand $aa_len\n",$cdsobj->seq(),"\n");
>
> $ss=Bio::Tools::SeqStats->new(-seq => $codobj);
>
> $refcount = $ss->count_codons();
>
> foreach $codon (keys(%$refcount)) {
> print("$codon   $refcount->{$codon}\n");
> }
> }
>
> ### script end ###
>
> Cheers
>
> Govind
> John Innes Centre
> Norwich UK.
>
>
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_ebi _ac _uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambridge, CB10 1SD, United Kingdom
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