[Bioperl-l] usage question, Genemark parser

[Thomas Keller]

Greetings,
I thought I would try the Genemark parser (Bio/Tools/Genemark.pm) with 
the prokaryotic model output, though the authors warn it may not work. 
I can dump the @exon_arr and it contains the location info, but then 
what? I'm stuck on the usage. (... I am new to using OOP)
here's the code:
use strict;
use Bio::Tools::Genemark;
use Bio::Seq;

my $results = $ARGV[0] ;

# genome sequence file from which I hope to extract the CDS segments
my $source = "~/Documents/Consults/GenePrediction_out/0209_cat1_37.fa";

my $Genemark = Bio::Tools::Genemark->new(-file => $results);
my $seqio = Bio::SeqIO->new( -format => 'embl', -file => "$source");
my $seqobj = $seqio->next_seq();

while(my $gene = $Genemark->next_prediction()) {
	my @exon_arr = $gene->exons();
     foreach my $cds (@exon_arr) {
     	#use the location info
     	#to get the sequence string from the $seqobj
     	#how?
     }
}

# the next step is to design primers for each putative gene sequence. 
I'd love suggestions for that as well.

__DATA__
the  prokaryotic output looks like:

GeneMark.hmm PROKARYOTIC (Version 2.1)
Sequence file name: sequence,	RBS: Y
Model file name: pseudonative.mod_iteration_4
Model organism: Pseudonative.model
Wed Jan 15 14:38:57 2003

Predicted genes
    Gene    Strand    LeftEnd    RightEnd       Gene     Class
     #                                         Length
     1        -           1         591          591        1
     2        -         605         940          336        1
     3        -        1631        1726           96        1
     4        -        2401        2853          453        1
     5        +        3104        3697          594        1
     6        +        3703        3897          195        1
     7        -        4061        4708          648        1

Thanks for your help.
Tom K
Tom Keller, Ph.D.
http://www.ohsu.edu/core
kellert at ohsu.edu
503-494-2442