[Bioperl-l] Bioperl Entrez Esearch

Smithies, Russell Russell.Smithies at agresearch.co.nz
Tue Jul 21 16:34:31 EDT 2009

Someone mentioned using try-catch a while ago for catching errors,  it might work in this case:

#!perl -w
use Error qw(:try);

try {
   $seqio = Bio::SeqIO->new(-file='my.fas');
catch Error with {
   my $e = shift;
   # $e->test will contain the message

Or you could redirect STDERR to a file:

         open(STDERR, ">", "$logfile") or die "Failed to re-direct STDERR to '$logfile': $!";

Or you could try using the "no warnings" pragma

Hopefully, one of these will work  :)


From: Rajasekar Karthik [mailto:karthik085 at gmail.com]
Sent: Wednesday, 22 July 2009 3:07 a.m.
To: Smithies, Russell
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Bioperl Entrez Esearch

Russell / Others,
The utilities keep printing out warnings and errors. Is there any way to
a) either not print at all
b) or send them to some other log file other than apache's error.log

On Wed, Jul 15, 2009 at 5:34 PM, Rajasekar Karthik <karthik085 at gmail.com<mailto:karthik085 at gmail.com>> wrote:
that helps - thanks!!!

On Tue, Jul 14, 2009 at 6:33 PM, Smithies, Russell <Russell.Smithies at agresearch.co.nz<mailto:Russell.Smithies at agresearch.co.nz>> wrote:
You sure can.
Take a look at http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org<mailto:bioperl-l-bounces at lists.open-bio.org> [mailto:bioperl-l-<mailto:bioperl-l->
> bounces at lists.open-bio.org<mailto:bounces at lists.open-bio.org>] On Behalf Of Rajasekar Karthik
> Sent: Wednesday, 15 July 2009 10:23 a.m.
> To: bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org>
> Subject: [Bioperl-l] Bioperl Entrez Esearch
> Hi,
> I an new to Bioperl. How can I do an Entrez Esearch using Bioperl?
> For example, I want to do an exact title search in pubmed
> Title: Guidelines for quantitative rt-PCR
> Using HTTP Get, I would do something like this
> URL:
> http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&field=titl&te
> rm=Guidelines%20for%20quantitative%20rt-PCR
> to get the response XML.
> How can I use Bioperl to do the above action?
> Thanks.
> --
> Best Regards,
> Rajasekar Karthik
> karthik085 at gmail.com<mailto:karthik085 at gmail.com>
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Best Regards,
Rajasekar Karthik
karthik085 at gmail.com<mailto:karthik085 at gmail.com>

Best Regards,
Rajasekar Karthik
karthik085 at gmail.com<mailto:karthik085 at gmail.com>

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