[Bioperl-l] translate() oddities

Derek Gatherer d.gatherer at mrcvu.gla.ac.uk
Tue Apr 29 10:05:03 EDT 2008


Thanks Stefan

Actually, there was a typo in my message, I did use -frame => 
1.  However, the problem disappears on upgrading from 1.5.0 to 1.5.2.

So not a bug anymore.

Cheers
Derek

At 14:46 29/04/2008, Stefan Kirov wrote:
>my $frame1_obj = $seqobj->translate(-frame => 1);
>not
>my $frame1_obj = $seqobj->translate(frame => 1);
>Stefan
>
>Derek Gatherer wrote:
> > Hi
> >
> > I thought I'd better run this by the community before I embarrass
> > myself on Bugzilla.  It seems like a clear bug to me.  I'm running
> > Bioperl 1.5.0 on RedHat.
> >
> > For a test input:
> >
> > >test
> > ATGATGATGATGATGTGA
> >
> > the following code is fine.
> >
> > while((my $seqobj = $seq_in->next_seq()))
> > {
> >     print "\n".$seqobj->display_id;
> >     my $len  = $seqobj->length();
> >     print " length: $len";
> >     my $frame1_obj = $seqobj->translate();
> >     my $f1_prot = $frame1_obj->seq();
> >     print "\n$f1_prot";
> > }
> >
> > Output:
> >
> > test length: 18
> > MMMMM*
> >
> > But if I want to change the frame as specified in the BioPerl
> > tutorial, by using:
> >
> > my $frame1_obj = $seqobj->translate(frame => 1); # which should now
> > give frame 2, I get:
> >
> > test length: 18
> > MMMMM-frame
> >
> > The frame is unchanged and the text "-frame" is tacked on the end of
> > the output.  The same occurs with translate(frame => 2).
> >
> > Any ideas?  Can something as fundamental as translate() really be
> > bugged?  or am I guilty of some particularly heinous syntax error?
> >
> > Cheers
> > Derek
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >



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