[Bioperl-l] Bio:Seq->translate with orf=1; behavior change between 1.5 and 1.6

[Mark A. Jensen]

Colin - This looks like a bug; the pod states

  "if you want translate() to find the first initiation
   codon and return the corresponding protein:

   $protein_seq_obj = $cds_seq_obj->translate(-orf => 1);"

but the orf-finding routine appears to stop at the first _termination_
codon (which is at bp 8 - TAA) and kicks out the "orf" M*.

I have created https://github.com/bioperl/bioperl-live/issues/105.

(Good test sequence, BTW)

MAJ



On 2015-03-03 20:13, Wilson, Colin (CC) wrote:
> I've got an older application that I'm migrating from BioPerl 1.5 to
> 1.6.923, and it didn't pass testing due to a change in the behavior 
> of
> Bio:Seq::translate between 1.5 and 1.6
>
> Per  the bioperl documentation Seq->translate(-orf=> 1) should return
> the first orf in a sequence.   It appears to be returning the orf
> upstream of the first stop codon, so an internal out of frame orf is
> found instead of a full length orf.
>
> Here's my test code.   It passes in 1.5, fails in 1.6.  Is there a
> switch or different parameter to get the old behavior?  Is this a bug
> or intentional change in translate?
> ------------
> use strict;
> use Bio::Seq;
>
> my ($bs, $prot, $orf0, $orf1, $orf) ;
> $bs = Bio::Seq->new( -seq           => "ATGAATGTAAATAA",
> 		   -display_id       => "TestSequence",
> 		   -alphabet         => 'dna' );
>
> $orf0 = $bs->translate(-frame=>0);
> $orf1 = $bs->translate(-frame=>1);
>
> # should output MNVN orf that starts in frame 0, not M* orf that
> starts in frame 1
> $orf = $bs->translate(-orf=>1, -start=> 'atg');
> if ($orf0->seq eq $orf->seq) {
>         print "PASS";
> }
> else {
>     print $orf0->seq . " != " . $orf->seq . "\n";
> }
>
>
>
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