[Bioperl-l] get geneID for gene names

[Fields, Christopher J]

Hermann,

The below works for me (note I'm using esearch, not efetch).  To actually get the records you will use efetch and the IDs obtained below.

chris

------------------------------
my $name = "Copg";
my $factory = Bio::DB::EUtilities->new(-eutil  => 'esearch',
                                      -db     => 'unists',
                                      -term   => '$name AND mouse [ORGN]',
                                      -email  => '<EMAIL_HERE>',
                                      );

print join(',',$factory->get_ids)."\n";


On May 2, 2012, at 12:42 PM, Hermann Norpois wrote:

> Hello,
> 
> I wish to get gene IDs for gene names (e.g. bdnf, copg). I thought it was a
> good idea to use Bio::DB::EUtilities (see below) and addressed UNISTS as
> database because there it was quite easy to find the gene ID. So far I was
> unable to retrieve the gene ID from UNISTS. Could anybody give me a hint
> how to proceed? The cookbook ... Yes, I was trying.
> 
> #!/bin/perl -w
> 
> use Bio::DB::EUtilities;
> 
> my $name = "Copg";
> my $factory = Bio::DB::EUtilities->new(-eutil  => 'efetch',
>                                       -db     => 'unists',
>                                       -term   => '$name AND mouse [ORGN]',
>                                       -email  => 'hnorpois at mpipsykl.mpg.de'
>                                       )
> 
> 
> Thank you
> Hermann Norpois
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