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

Krys Kelly kak28 at cam.ac.uk
Wed Sep 20 09:49:49 EDT 2006


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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