[Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS
cgoddard at flmnh.ufl.edu
Wed Jan 28 17:31:48 EST 2009
Thank you. I was finally able to figure it out. I'm a bit embarrassed
to say this, but the problem was that I was not specifying the database
to query when I did the get_Stream_by_query() call, and it was returning
results from a database without that coding sequence completion
information in the definition.
Jason Stajich wrote:
> where is the information in the genbank record (as a text file)?
> DEFINITION ?
> On Jan 28, 2009, at 10:02 AM, Christopher Goddard wrote:
>> I need to determine if a Bio::Seq object returned from GenBank by a
>> Bio::DB::GenBank->get_Stream_by_query() call is a partial or complete
>> coding sequence. This information is given in the description for a
>> sequence when performing a search on Entrez. However, using the
>> method desc() for the sequences returned doesn't relay this
>> information, at least not all of the time. If someone could point me
>> in the right direction on where I could retrieve this information I
>> would be really appreciative.
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org <mailto:Bioperl-l at lists.open-bio.org>
> Jason Stajich
> jason at bioperl.org <mailto:jason at bioperl.org>
IT Expert, Informatics
Florida Museum of Natural History
University of Florida
Gainesville, FL 32611
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