Bioperl: Re: GFFconversion (fwd)

[Ewan Birney]

On Fri, 14 Jan 2000, Richard Bruskiewich wrote:

> Hello everyone:
> 
> Have any of you coded such a beast in EnsEMBL, Bioperl or raw Perl 
> (or similar) yet? I haven't (yet) had the time to do the job in EMBOSS.

In the bioperl main trunk there is easy embl/genbank -> gff via the
annseq and annseqio objects.

read in an annseq - loop over features - print gff_string.



> 
> Cheers,
> ========================================================
> Dr. Richard Bruskiewich		<rbsk@sanger.ac.uk>
> 	WWW: http://www.sanger.ac.uk/Users/rbsk/
> Human Analysis/Bioinformatics
> The Sanger Centre		Tel:  +44-(0)1223-834244
> Wellcome Trust Genome Campus,	Fax:  +44-(0)1223-494919
> Hinxton, Cambridge   CB10 1SA
> United Kingdom
> ========================================================
> 
> ---------- Forwarded message ----------
> Date: Thu, 13 Jan 2000 13:11:27 +0100
> From: mplatzer <mplatzer@imb-jena.de>
> To: rbsk@sanger.ac.uk
> Subject: GFFconversion
> 
> Dear Richard,
> 
> I'm wondering whether there are GFF conversion utilities available other
> than ACDB2GFF and the tools from Ian Holmes?
> 
> I would be particularly interested in the conversion from
> GenBank/EMBL/ASN.
> 
> Thank you in advance,
> 
> 
> Matthias Platzer
> 
> Department of Genome Analysis
> Institute of Molecular Biotechnology
> P.O.Box  100813, D 07708 Jena
> voice : int+49.3641.656254
> fax   : int+49.3461.656255
> E-mail: mplatzer@imb-jena.de
> www   : http://genome.imb-jena.de/
> 
> 
> 
> 
> 

-----------------------------------------------------------------
Ewan Birney. Work: +44 (0)1223 494992. Mobile: +44 (0)7970 151230
<birney@sanger.ac.uk>
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