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

[Christine Hoogland]

Hi Chris,

Thanks a lot for your fast answer. I updated BioPerl with
cpan -i 'Bio::Seq'
and I have now 1.006922

and the translation is working as expected!
with complete_codons: translate to NPLG
without (default): translate to NPL

Previously I installed following instructions at 
http://www.bioperl.org/wiki/Installing_BioPerl_on_Ubuntu_Server

and didn't realised it was referring to current_core_unstable.tar.bz2... 
probably not the latest version!!

Thanks again!
Christine

On 30/01/14 12:42, Fields, Christopher J wrote:
> 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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>> Bioperl-l at lists.open-bio.org
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>

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