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

[Fields, Christopher J]

I think may be related to changes related to issues with frame.  I’ll post this to github in the meantime and see if I can bisect this.

chris

> On Mar 3, 2015, at 6:13 PM, Wilson, Colin (CC) <CCWilson at dow.com> 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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