[Bioperl-l] How to get rid of warnings

Niels Larsen niels at genomics.dk
Fri Aug 18 11:28:48 EDT 2006


I am a casual user of bioperl with my own error handling. Is there
a way to switch off bioperls error handling? I switch off my own
with

$Common::Config::with_errors = 0;
$Common::Config::with_warnings = 0;

Sendu Bala wrote:
> Jérémy JUST wrote:
>>     Hello,
>>
>>   I can't manage to get rid of all warnings during a query from GenBank
>> with BioPerl 1.4. When the query doesn't give any result, I catch the
>> exception, but there is still a warning that is issued to STDERR.
> [...]
>> and the unwanted warning is:
>> <<<<<
>> Warning(s) from GenBank: 
>>                 <PhraseNotFound>FooBar</PhraseNotFound>
>>
>>   How could I set verbosity so that I don't get this warning?
> 
> You can't easily or appropriately do it with bioperl 1.4, but I've just 
> fixed the problem in cvs. You might be able to just download revision 
> 1.18 of Bio/DB/Query/GenBank.pm from bioperl-live:
> 
> http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/Bio/DB/Query/
> 
> (The perl hack would be to redirect STDERR to /dev/null inside your eval.)
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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> 

-- 
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Niels Larsen
Danish Genome Institute
Gustav Wieds vej 10 C
DK-8000 Aarhus C
Denmark

Electronic mail: niels at genomics.dk
Skype: niels_larsen_denmark

Telephone: +45-8942-5268
Telefax: +45-8620-1222

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