[Bioperl-l] Gene Type in Entrez gene?

[Carnë Draug]

On 28 September 2011 07:03, Jill <jillianrowe91286 at gmail.com> wrote:
> Hi there,
>
> I am using the Bio::DB::Eutilities module to download gene sequences
> based on a query.
>
> <code>
> [...]
> }
> </code>
>
> Then I go on to use genbank to download the sequences based on the
> chromosome splice. For what I have it works great. But I am trying to
> get to the gene type (either protein coding or pseudo) as well. I can
> see it in the summary on the Entrez Gene sight, but can't get to it
> through bioperl. When I have it print out all the contents of the
> summary it doesn't show up there either.
>
> Any help?

Hi Jill,

there's already a script in bioperl that does what you want, it's just
not part of the current stable release. You can get it here

https://github.com/bioperl/bioperl-live/blob/master/scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl

You can download the script alone, it will work fine in previous
releases of bioperl, no need to write another one.

Carnë Draug