[Bioperl-l] Re: EMBL / GenBank to GFF

[Lincoln Stein]

You can use Bioperl to do that.  The script will look like this:

	use Bio::SeqIO;
	my $embl_file = shift;
	my $in = Bio::SeqIO->new(-file=>$embl_file,-format=>'EMBL');
	while (my $seq = $in->next_seq) {
		for my $feat ($seq->top_SeqFeatures) {
			print $feast->gff_string,"\n";
		}
	}

You can find Bioperl at www.bioperl.org

Lincoln
	


On Friday 05 July 2002 12:05 pm, Alessandro Guffanti wrote:
> Hi - is there any utility for converting GenBank - EMBL
> Flat files in GFF? I can't find it in the web site.
>
> Best of all,
>
> Alessandro Guffanti
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Alessandro Guffanti - Bioinformatics
> FIMO - FIRC Institute of Molecular Oncology
> Via Adamello, 16 - 20139 Milano, Italy
> Ph.: +39-02.574.303.233  Fax: +39-02.574.303.244
> http://www.ifom-firc.it  guffanti@ifom-firc.it

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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