[Bioperl-l] skip "exception"

[Hilmar Lapp]

Note that this is a warning, not an exception. Or so it should be. 
I.e., you won't have that feature in your feature array and have a 
nasty looking message printed on your terminal, but otherwise the 
program/script should run just fine and return a perfectly legal 
Bio::SeqI object.

	-hilmar

On Sunday, September 26, 2004, at 10:18  AM, Stefan Kirov wrote:

> 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
>
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>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------