[Bioperl-l] Bio::Tools::Genemark question

[Charles Hauser]

Hi,

I'm trying to generate GFF files from GeneMark gene model predictions.

Problem is my script is not parsing the last gene entry in the file.

In example below, script fails to parse gene #63.  I tried appending a
duplicate copy of the gene 63 data to the end of the file (2 copies) to
no avail. 

Charles



synopsis:

my $Genemark = Bio::Tools::Genemark->new(-file => $infile);

while(my $gene = $Genemark->next_prediction()) {
    foreach my $feat (@exon_arr) {
	my @tags = $feat->get_all_tags();
	$feat->seq_id($scaffold);
	$feat->source_tag('GeneMark');
	$feat->add_tag_value('genemark','genemark_'.$num_scaffold .".".$ver);
	$gffout->write_feature($feat);
    }
}


data:

GeneMark.hmm (Version 2.2a)
Sequence name: scaffold_1
Sequence length: 376197 bp
G+C content: 64.06%
Matrix: Chlamydomonas reinhardtii
Wed Apr 23 15:35:57 2003

Predicted genes/exons

Gene Exon Strand Exon           Exon Range     Exon      Start/End
  #    #         Type                         Length       Frame

  1     3   -  Terminal      8808      8854      47          3 2
  1     2   -  Internal      8962      9023      62          1 3
  1     1   -  Initial       9198      9226      29          2 1

<snip>


 62     1   +  Initial     364788    364821      34          1 1
 62     2   +  Internal    365037    365139     103          2 2
 62     3   +  Internal    365362    365419      58          3 3
 62     4   +  Internal    365848    365950     103          1 1
 62     5   +  Internal    366152    366225      74          2 3
 62     6   +  Internal    366671    366827     157          1 1
 62     7   +  Internal    367066    367219     154          2 2
 62     8   +  Internal    367915    368032     118          3 3
 62     9   +  Terminal    368348    368359      12          1 3

 63     2   -  Terminal    369209    369289      81          3 1
 63     1   -  Internal    369503    369719     217          3 3