[Bioperl-l] EMBL release 87 format changes.

Chris Fields cjfields at uiuc.edu
Wed Jun 21 15:00:02 EDT 2006


That would be great!  Post a patch/fix via bugzilla:

http://www.bioperl.org/wiki/HOWTO:SubmitPatch

and we can add it and test it out.  Or if you have CVS access you can do it
yourself.  Not sure who's taking care of SeqIO::embl at the moment....

Added bit : you'll need to update both next_seq and write_seq.  next_seq
should probably handle both old and new EMBL format and write_seq should
only write new format (unless someone else disagrees???)

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of dwaner at scitegic.com
> Sent: Wednesday, June 21, 2006 1:14 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] EMBL release 87 format changes.
> 
> With release 87 of EMBL (June 19th, 2006), there have been some minor
> changes to the flat file record format. In particular, the SV (sequence
> version) tag has been moved from its own line to a field in the ID line.
> See http://www.ebi.ac.uk/embl/Documentation/changesdetails.html.
> 
> Is somone already working on updating the SeqIO::embl parser, or should I
> volunteer?
> 
> - David
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> Bioperl-l at lists.open-bio.org
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