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|
#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Gene_obj;
use GFF3_utils;
use Data::Dumper;
my $usage = "usage: $0 file.gff3\n\n";
my $gff3_file = $ARGV[0] or die $usage;
my %feat_types = ( intergenic => 0,
intron => 1,
'exon+' => 2,
'exon-' => 3,
'rRNA+' => 4,
'rRNA-' => 5,
);
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);
foreach my $asmbl_id (sort keys %$contig_to_gene_list_href) {
my @pos_vec;
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 $isoform ($gene_obj_ref, $gene_obj_ref->get_additional_isoforms()) {
my @introns = $isoform->get_intron_coordinates();
foreach my $intron (@introns) {
my ($lend, $rend) = sort {$a<=>$b} @$intron;
for (my $i = $lend; $i <= $rend; $i++) {
if ( (! defined $pos_vec[$i]) || $pos_vec[$i] < $feat_types{intron}) {
$pos_vec[$i] = $feat_types{intron};
}
}
}
my $orient = $isoform->get_orientation();
my $feat_type = "exon$orient";
if ($isoform->{com_name} =~ /rrna/i && ! $isoform->has_CDS()) {
$feat_type = "rRNA$orient";
}
my @exons = $isoform->get_exons();
foreach my $exon (@exons) {
my ($lend, $rend) = sort {$a<=>$b} $exon->get_coords();
for (my $i = $lend; $i <= $rend; $i++) {
if ( (! defined $pos_vec[$i]) || $pos_vec[$i] < $feat_types{$feat_type}) {
$pos_vec[$i] = $feat_types{$feat_type};
}
}
}
}
}
shift @pos_vec; #rid first position, since we were using 1-based coordinates above.
foreach my $pos (@pos_vec) {
unless (defined $pos) {
$pos = 0;
}
}
my $pos_string = join("", @pos_vec);
$pos_string =~ s/(\S{60})/$1\n/g;
print ">$asmbl_id\n$pos_string\n";
}
exit(0);
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