[Bioperl-l] extract info from .game.xml

Tuan A. Tran tuantran167 at gmail.com
Tue Jun 14 20:03:47 EDT 2005


I am trying to extract some information from a file filename.game.xml
(I got this file from flybase.org). I wrote a simple script to test
it. However, I keep getting the following message

------------- EXCEPTION  -------------
MSG: No annotations
STACK Bio::SeqIO::game::gameHandler::load
STACK Bio::SeqIO::game::_getseqs
STACK Bio::SeqIO::game::next_seq
STACK toplevel fetchseq_game_xml.pl:64

I have no idea why. Can anyone help?
Thanks in advance,

My simple script is


use strict;

sub NULL () {0};

use Bio::Seq;
use Bio::SeqIO;
#use Bio::SeqIO::game;
#use Bio::Annotation;
use Bio::SearchIO;
use Bio::AlignIO;
use Bio::SimpleAlign;
use Bio::LocatableSeq;
use Bio::Tools::Run::StandAloneBlast;
use Bio::Tools::Run::Alignment::Clustalw;
use Getopt::Long;
use Bio::DB::GenBank;
use Bio::DB::Flat::BDB;
#use Bio::Index::GenBank;
use Bio::Index::Fasta;
use Bio::SeqFeature::Generic;
use DBI;

my $infile = shift;
my $in = Bio::SeqIO->new( -file=> $infile, -format=>'game');

while (my $query = $in->next_seq() ) {

	print $query->id,"\n";

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