[Bioperl-l] Extracting gene seq from Bio::DB::GFF

Scott Cain cain at cshl.edu
Fri Aug 11 15:05:54 EDT 2006


Hi Marco,

What you are getting from get_feature_by_name is a list of
Bio::DB::GFF::Feature objects, which are Bio::SeqFeatureI objects.  What
you need are Bio::PrimarySeq objects.  Fortunately,
Bio::DB::GFF::Feature has a method to get a PrimarySeq out of it; that
method is called seq.

So, you should be able to change your line to

  $out->write_seq( $_->seq() ) for @feat;

and it should work.  Of course, I haven't test that to make sure that it
does :-)

Scott


On Fri, 2006-08-11 at 11:30 -0700, Marco Blanchette wrote:
> Dear all,
> 
> I used to use this very simple script to extract the gene sequence as a
> fasta flat file from a Bio::DB::GFF database containing the GadFly 4.3
> annotations
> 
> #!/usr/bin/perl
> 
> use strict;
> use warnings;
> use Bio::DB::GFF;
> use Bio::SeqIO;
> 
> my $out = Bio::SeqIO->new(    -fh => \*STDOUT,
>                             -format => 'fasta');
> 
> my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql',
>                               -dsn => 'dbi:mysql:database=dmel_43_LS');
> 
> while (<>){
>     chomp;
>     my @feat = $db->get_feature_by_name($_);
>     $out->write_seq($_) for @feat;
> }
> 
> Somehow I now get the following output instead of the actual sequences:
> >FBgn0024988 gene:.(FBgn0024988)
> Bio::PrimarySeq=HASH(0x19fd3d8)
> >FBgn0041184 gene:.(FBgn0041184)
> Bio::PrimarySeq=HASH(0x19fa684)
> >FBgn0033636 gene:.(FBgn0033636)
> Bio::PrimarySeq=HASH(0x19e1908)
> 
> What change and what would be the right way to get what I want?
> 
> Many thanks
> 
> Marco
> ______________________________
> Marco Blanchette, Ph.D.
> 
> mblanche at uclink.berkeley.edu
> 
> Donald C. Rio's lab
> Department of Molecular and Cell Biology
> 16 Barker Hall
> University of California
> Berkeley, CA 94720-3204
> 
> Tel: (510) 642-1084
> Cell: (510) 847-0996
> Fax: (510) 642-6062
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory
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