[Bioperl-l] Bioperl Entrez Esearch

[Chris Fields]

Hopefully most of those warnings are server-side issues and not my  
bugs! ;>

If there are warnings you can turn them off ($obj->verbose(-1)).  You  
can also use ultrastrict verbose(2), which converts everything to an  
exception, and then a simple eval block or try/catch (latter if you  
have Error.pm) should work (I don't think try/catch works with  
warnings,  but I know an eval block won't).

chris

On Jul 21, 2009, at 3:34 PM, Smithies, Russell wrote:

> 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
> http://search.cpan.org/~nwclark/perl-5.8.9/lib/warnings.pm
>
>
> Hopefully, one of these will work  :)
>
> --Russell
>
>
>
> 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
>
> Thanks.
> 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
>
>
> --Russell
>
>> -----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>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org<mailto:Bioperl-l at lists.open-bio.org>
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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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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