[Bioperl-l] how to suppress Bioperl exceptions

Hilmar Lapp hlapp at gmx.net
Sat Apr 11 11:56:35 EDT 2009

Hi Jarod,

in addition to Mark's response, what you say in your message would  
mean that corruption is in specific entries of a file and you want to  
skip those, rather than entire files.

If this is true, then you'd have to put the $seq=$seqio->next_seq()  
call into the try {} block as that'd be the one that would raise the  
exception. The SeqIO parsers don't generally guarantee though that  
they will gracefully recover from a parsing error and advance to the  
next record; I think the genbank parser will do that, but you will  
definitely want to check that.


On Apr 11, 2009, at 9:50 AM, ÔÆ ºÎ wrote:

> Hi, all,
> I use Bio::SeqIO driver to parse data files. The input data is  
> somewhat buggy, and some of entries are not strict in format. The  
> parser will throw exceptions and halt when meeting these bad  
> entries. However, I want to just skip these entries, not stop there.  
> So how to suppress exceptions?
> Thanks.
> Jarod
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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