[Bioperl-l] how to suppress Bioperl exceptions

[Hilmar Lapp]

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.

	-hilmar

On Apr 11, 2009, at 9:50 AM, 云 何 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
>
>
>
>      ___________________________________________________________
>  好玩贺卡等你发，邮箱贺卡全新上线！
> http://card.mail.cn.yahoo.com/
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================