1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
|
#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
use lib ("$FindBin::Bin/../PerlLib");
use Gene_obj;
use GFF3_utils;
use Carp;
use Nuc_translator;
use File::Basename;
my $usage = "\n\nusage: $0 gff3_file\n\n";
my $gff3_file = $ARGV[0] or die $usage;
my $gene_obj_indexer_href = {};
## associate gene identifiers with contig id's.
my $contig_to_gene_list_href = &GFF3_utils::index_GFF3_gene_objs($gff3_file, $gene_obj_indexer_href);
print "track name=\'" . basename($gff3_file) . "\'\n";
foreach my $asmbl_id (sort keys %$contig_to_gene_list_href) {
my @gene_ids = @{$contig_to_gene_list_href->{$asmbl_id}};
foreach my $gene_id (@gene_ids) {
my $gene_obj_ref = $gene_obj_indexer_href->{$gene_id};
foreach my $gene ($gene_obj_ref, $gene_obj_ref->get_additional_isoforms()) {
my $bed = $gene->to_BED_format();
print $bed;
}
}
}
exit(0);
|
