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

[Fields, Christopher J]

Glad to hear it worked out!

chris

On Jan 29, 2014, at 9:18 PM, Christine Hoogland <christine.hoogland at gmail.com> wrote:

> 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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> -- 
> Christine Hoogland
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