[Bioperl-l] skip "exception"

Qunfeng qfdong at iastate.edu
Sun Sep 26 11:13:48 EDT 2004


When I try to use Bioperl to parse genbank sequence file downloaded from 
NCBI, I am getting the following "exception" with sequence (acc# AJ635582). 
It seems to be the format problem in this genbank file.

My question is: is there any way in bioperl for users to test if there is 
any format problem in the sequence object and then decide by the users if 
they want to throw an exception or simply skips to the next object? Thanks!


-------------------- WARNING ---------------------
MSG: exception while parsing location line [1163^1163] in reading 
EMBL/GenBank/SwissProt, ignoring feature variation (seqid=AJ6355
------------- EXCEPTION  -------------
MSG: Only adjacent residues when location type is IN-BETWEEN. Not [1163] 
and [1163]
STACK Bio::Location::Simple::location_type 
STACK Bio::Location::Simple::new 
STACK Bio::Factory::FTLocationFactory::_parse_location 
STACK Bio::Factory::FTLocationFactory::from_string 
STACK (eval) /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:124
STACK Bio::SeqIO::FTHelper::_generic_seqfeature 
STACK Bio::SeqIO::genbank::next_seq 

More information about the Bioperl-l mailing list