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

[Mark A. Jensen]

Hi Colin,
This is now fixed (I hope) at 
https://github.com/bioperl/bioperl-live/commit/9fb341c333b6b532308ebb4f2feef5a90382aab7. 
Added a couple of tests to t/Seq/PrimarySeq.t to make sure. If you look 
at the commit, it's pretty easy to patch Bio/PrimarySeqI.pm by hand (not 
ideal...but...sigh)
(CJF - is it worth patching the 1.6.924 tag?)
MAJ

On 2015-03-16 23:08, Mark A. Jensen wrote:
> 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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