[Bioperl-l] get geneID for gene names

[Hermann Norpois]

Thank you very much. But there still is a problem.

This is my output:
525211,210532,167498,142652

I get some ids (the first one is the UniSTS ID, the following ... I do not
know) but there is no gene ID. If you compare to the following link:
http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=525211 The gene ID
should be 54161<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=54161>
.

This is my (your) script:

#!/bin/perl -w

use Bio::DB::EUtilities;

my $name = "Copg";
my $factory = Bio::DB::EUtilities->new(-eutil  => 'esearch',
                                     -db     => 'unists',
                                     -term   => "$name AND Mus musculus
[ORGN]",
                                     -email  => 'hnorpois at mpipsykl.mpg.de',
                                     );

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



2012/5/2 Fields, Christopher J <cjfields at illinois.edu>

> Also, a small but very significant bug is in the below.  Can you spot it?
>
> The '-term' value is in single quotes, these need to be double-quotes to
> interpolate $name.  Otherwise, it is literally looking for '$name'.
>
> chris
>
> On May 2, 2012, at 12:55 PM, Christopher Fields wrote:
>
> > 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
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>