[Bioperl-l] Conversion of EMBL format flat file to GFF format flatfile

Chris Fields cjfields at uiuc.edu
Wed Sep 20 11:08:16 EDT 2006


It depends on what version of GFF you want.  I have only seen GenBank to
GFF; you could probably convert EMBL->GenBank->GFF.  If so I would recommend
updating your local bioperl installation from CVS to deal with recent
changes to the EMBL and GenBank SeqIO modules which makes them a bit more
compatible with one another.

Here are some scripts, which can also be found in the scripts directory when
you download the full bioperl core distribution.  

http://www.bioperl.org/wiki/Bioperl_scripts#Bio::DB::GFF

Just a warning: I think Lincoln and Scott are both working in having better
GFF3 integration with Bioperl.  Hopefully he or Scott Cain will also answer
this post to get you up-to-date, and maybe offer a few extra suggestions. 

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Krys Kelly
> Sent: Wednesday, September 20, 2006 8:50 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Conversion of EMBL format flat file to GFF format
> flatfile
> 
> I am completely new to Bioperl.  I would like to convert an EMBL flat file
> into a GFF flat file. To make sure I could get a perl script to work I
> have
> used the following script to read in my EMBL file and write it out as
> FASTA:
> 
> 
> 
> my $in  = Bio::SeqIO->new(-file => "Toxo1b_080605_test.embl",
> 
>                        -format => 'EMBL');
> 
> my $out = Bio::SeqIO->new(-file => ">ChrIb_new.fasta",
> 
>                        -format => 'fasta');
> 
> while ( my $seq = $in->next_seq() ) {$out->write_seq($seq); }
> 
> 
> 
> But the list of formats available
> (http://bioperl.open-bio.org/wiki/HOWTO:SeqIO#Formats ) does not contain
> gff.
> 
> 
> 
> I have tried searching the documentation and the mail archives, but I have
> not found anything that would help me. Are there any existing bioperl
> modules for this conversion? I would be grateful for any help.
> 
> 
> 
> Thanks
> 
> 
> 
> Krys
> 
> 
> 
> 
> 
> Dr Krystyna A Kelly (Krys)
> 
> 
> 
> 
> Department of Pathology
> 
> and
> 
> MRC Biostatistics Unit
> 
> 
> University of Cambridge
> 
> 
> 
> Institute of Public Health
> 
> 
> Tennis Court Road
> 
> 
> 
> Robinson Way
> 
> 
> Cambridge CB2 1QP
> 
> 
> 
> Cambridge CB2 2SR
> 
> 
> 01223 333331
> 
> 
> 
> 01223 767408
> 
> 
> kak28 at cam.ac.uk
> 
> 
> 
> krystyna.kelly at mrc-bsu.cam.ac.uk
> 
> 
> 
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