[Bioperl-l] EMBL access through bioperl

[Heikki Lehvaslaiho]

Yes, there is Bio::DB::EMBL but it was not done in time to make into
0.7.0 release. The 0.7.X releases are only bug fixes, so it will be
included in 0.9 later this year.
If you need it now, you can check out bioperl-live from the CVS
repository. There are instrcutions in the website. An other option is
to go into WebCVS and copy it from there :

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/DB/EMBL.pm?cvsroot=bioperl

	-Heikki



"govind chandra (JIC)" wrote:
> 
> Hello,
> 
> I would like to know if there is a way to get EMBL files (from EBI or
> Heidelberg) similar to the way it is possible to get them from GenBank
> (Bio::DB::GenBank). I think I heard some mention of it on this list sometime
> back. I have Bioperl 0.7.1 and could not find any module for doing this.
> 
> I can get the files from GenBank and write them out as EMBL using Bio::SeqIO
> but have noticed that these files have an additional feature called 'gene'
> for every CDS (compared with the corresponding embl files got directly from
> EMBL). The conversion is perfect, it is just that the GenBank files have
> this additional feature called gene for every CDS. My scripts which write
> .ace files for reading into ACeDB rely for everything on bioperl and have
> been written with the EMBL format in mind. I could always make them ignore
> the feature gene but it will be nice if this format conversion could be
> avoided entirely.
> 
> I will appreciate any help in this regard.
> 
> Govind
> (Govind Chandra)
> ScoDB
> John Innes Centre
> Norwich
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________