[Bioperl-l] skip "exception"

[Stefan Kirov]

Sometimes it is not reasonable to continue after an error, but Qunfeng 
has a point. Maybe we can add to at least some parsers an option like 
-ignore=>{number of allowed exceptions}, warn if the parser generates 
less errors than tne number requested by the user, die if the number 
becomes greater.
Any thoughts on this?
Stefan

Qunfeng wrote:

> Hi,
>
> 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!
>
> Qunfeng
>
> -------------------- WARNING ---------------------
> MSG: exception while parsing location line [1163^1163] in reading 
> EMBL/GenBank/SwissProt, ignoring feature variation (seqid=AJ6355
> 82):
> ------------- EXCEPTION  -------------
> MSG: Only adjacent residues when location type is IN-BETWEEN. Not 
> [1163] and [1163]
> STACK Bio::Location::Simple::location_type 
> /usr/lib/perl5/site_perl/5.8.0/Bio/Location/Simple.pm:280
> STACK Bio::Location::Simple::new 
> /usr/lib/perl5/site_perl/5.8.0/Bio/Location/Simple.pm:95
> STACK Bio::Factory::FTLocationFactory::_parse_location 
> /usr/lib/perl5/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm:218
> STACK Bio::Factory::FTLocationFactory::from_string 
> /usr/lib/perl5/site_perl/5.8.0/Bio/Factory/FTLocationFactory.pm:157
> STACK (eval) /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:124
> STACK Bio::SeqIO::FTHelper::_generic_seqfeature 
> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/FTHelper.pm:123
> STACK Bio::SeqIO::genbank::next_seq 
> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/genbank.pm:501
>
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-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
1060 Commerce Park, Oak Ridge
TN 37830-8026
USA
tel +865 576 5120
fax +865 241 1965
e-mail: skirov at utk.edu
sao at ornl.gov