[Bioperl-l] How to get rid of warnings

Sendu Bala bix at sendu.me.uk
Fri Aug 18 11:04:57 EDT 2006


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.)


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