<commit_before>#!/usr/bin/perl -w
use strict;
use Bio::Tools::tRNAscanSE;
use Bio::Tools::GFF;

my $out = Bio::Tools::GFF->new(-gff_version => 3);
my $parser = Bio::Tools::tRNAscanSE->new(-file => shift);

# parse the results
while( my $gene = $parser->next_prediction ) {
     $out->write_feature($gene);
     for my $trans ( $gene->get_SeqFeatures() ) {	
	 $out->write_feature($trans,$trans->get_SeqFeatures());
    }

}
<commit_msg>exon and gene are the feature types we want<commit_after>#!/usr/bin/perl -w
use strict;
use Bio::Tools::tRNAscanSE;
use Bio::Tools::GFF;

my $out = Bio::Tools::GFF->new(-gff_version => 3);
my $parser = Bio::Tools::tRNAscanSE->new(-file => shift);

# parse the results
while( my $gene = $parser->next_prediction ) {
    my ($id) = $gene->get_tag_values('ID');
    $gene->primary_tag('gene');
    $out->write_feature($gene);
    my $i = 0;
     for my $trans ( $gene->get_SeqFeatures() ) {	
	 $trans->primary_tag('exon');
	 $out->write_feature($trans,$trans->get_SeqFeatures());
	 $i++;
    }

}

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{'dir': 'git-commits-cleaned', 'id': '6410261', 'n_tokens_mistral': 402, 'n_tokens_neox': 377, 'n_words': 75}