[Bioperl-l] How to stop rather than emit warnings with Bio::Das::segment?

[Fields, Christopher J]

Setting verbosity to 2 should convert warnings to exceptions.   

IIRC, set '-verbose => 2' in the Bio::Das constructor, set '$das->verbose(2)' explicitly, or set the env variable BIOPERLDEBUG=2.  

chris

________________________________________
From: bioperl-l-bounces at lists.open-bio.org [bioperl-l-bounces at lists.open-bio.org] on behalf of Peng Yu [pengyu.ut at gmail.com]
Sent: Friday, December 16, 2011 4:10 PM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] How to stop rather than emit warnings with Bio::Das::segment?

Hi,

Bio::Das::segment can give me the following warnings without stopping
the whole program when the position for the query doesn't exist. I
could test the return result and quit when it is []. But this would
cause my program have an test whenever I call segment. I'm wondering
if there is an automatic way to let Bio::Das::segment stop in such
cases.

--------------------- WARNING ---------------------
MSG: Sequence is not dna or rna, but []. Attempting to revcom, but
unsure if this is right
---------------------------------------------------


--
Regards,
Peng
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l