[Bioperl-l] Frame translation still gets an extra aa

[Fields, Christopher J]

The Bioperl version is wrong if you have v1.6.910; it should be something like 1.006910.  Do you have an older version of bioperl somewhere in your perl library path?  Try:

    perldoc -l Bio::Seq

chris

On Jan 29, 2014, at 8:08 PM, Christine Hoogland <christine.hoogland at gmail.com> wrote:

> Hi,
> 
> Back in 2011 there was a question/comment about frame translation behaviour:
> http://bioperl.org/pipermail/bioperl-l/2011-January/034422.html
> 
> I have perl v5.14.2 and BioPerl v.1.6.910, and still get this extra AA using or not the complete_codons option:
> 
> $ perl -MBio::Seq -e 'print "$Bio::Seq::VERSION\n";';
> 1.005002102
> 
> $ perl -l -MBio::Seq -e '$x=Bio::Seq->new(-display_id=>"foo",-seq=>"AAACCCTTTGGG"); print $x->translate(-frame=>1, -complete_codons => 1)->seq'
> NPLG
> 
> $ perl -l -MBio::Seq -e '$x=Bio::Seq->new(-display_id=>"foo",-seq=>"AAACCCTTTGGG"); print $x->translate(-frame=>1, -complete_codons => 0)->seq'
> NPLG
> 
> I would expect NPL only, when asking for codon not completed (complete_codons 0, supposed to be the default):
> a-aac-cct-ttg-gg
>  N   P   L
> 
> What am I doing wrong?
> Thanks,
> Christine
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