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

Krys Kelly kak28 at cam.ac.uk
Wed Sep 20 13:49:49 UTC 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


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.







Dr Krystyna A Kelly (Krys)


Department of Pathology


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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