[Bioperl-l] Frame translation still gets an extra aa
Fields, Christopher J
cjfields at illinois.edu
Thu Jan 30 04:21:20 UTC 2014
Glad to hear it worked out!
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!
> 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
>> On Jan 29, 2014, at 8:08 PM, Christine Hoogland <christine.hoogland at gmail.com> wrote:
>>> Back in 2011 there was a question/comment about frame translation behaviour:
>>> 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";';
>>> $ perl -l -MBio::Seq -e '$x=Bio::Seq->new(-display_id=>"foo",-seq=>"AAACCCTTTGGG"); print $x->translate(-frame=>1, -complete_codons => 1)->seq'
>>> $ perl -l -MBio::Seq -e '$x=Bio::Seq->new(-display_id=>"foo",-seq=>"AAACCCTTTGGG"); print $x->translate(-frame=>1, -complete_codons => 0)->seq'
>>> I would expect NPL only, when asking for codon not completed (complete_codons 0, supposed to be the default):
>>> N P L
>>> What am I doing wrong?
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
> Christine Hoogland
> 64/316 Long Street East
> Graceville QLD 4075
> Tel: +617 3129 9973
> Mobile: +614 7891 9833
> Email: christine.hoogland at gmail.com
> LinkedIn: http://ch.linkedin.com/pub/christine-hoogland/23/778/333
> Viadeo: http://www.viadeo.com/fr/profile/christine.hoogland
More information about the Bioperl-l