[Bioperl-l] BioPerl 1.6 and parsing multiple EMBL records

[Chris Fields]

On Jan 11, 2010, at 9:17 AM, Peter wrote:

> On Mon, Jan 11, 2010 at 3:04 PM, Mark A. Jensen <maj at fortinbras.us> wrote:
>> 
>> Hi Peter, I found the issue-- there are no SQ lines in the data, and having
>> them is a key stop condition in the parser (line 438 embl.pm).
>> We evidently need to be more liberal in what we accept, even as we are
>> strict in what we emit. Could you make a bug report?
>> thanks for the heads-up--
>> MAJ
> 
> Done: http://bugzilla.open-bio.org/show_bug.cgi?id=2982
> 
> These are EMBL contig records, so they don't have SQ lines,
> but instead CO lines.
> 
> Peter

Peter, 

Just curious, but have you tried the experimental EMBL parser 'embldriver'?  I don't think it's bound to the same strictures, but I may be mistaken.

chris