[Bioperl-l] get geneID for gene names

[Fields, Christopher J]

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
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>