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|
#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Gene_obj;
use Fasta_reader;
use GFF3_utils;
use Carp;
use Nuc_translator;
use Data::Dumper;
my $usage = "\n\nusage: $0 gff3_file utr_trim_dat [DEBUG]\n\n";
my $gff3_file = $ARGV[0] or die $usage;
my $utr_trim_dat = $ARGV[1] or die $usage;
my $DEBUG = $ARGV[2] || 0;
my %utr_trim_info;
{
open (my $fh, $utr_trim_dat) or die $!;
while (<$fh>) {
chomp;
my ($acc, $coords, @rest) = split(/\t/);
my ($lend, $rend) = split(/-/, $coords);
$utr_trim_info{$acc} = [$lend, $rend];
}
close $fh;
}
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 @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};
my $trimmed_flag = 0;
foreach my $isoform ($gene_obj_ref, $gene_obj_ref->get_additional_isoforms()) {
if ($isoform->has_UTRs()) {
my $isoform_acc = $isoform->{Model_feat_name};
if (my $trim_coords_aref = $utr_trim_info{$isoform_acc}) {
my $cdna_len = $isoform->get_cDNA_length();
my $targeted_cdna_len = $trim_coords_aref->[1] - $trim_coords_aref->[0] + 1;
print "\n====\nBefore:\n" . $isoform->to_GFF3_format() . "\n" if $DEBUG;
$isoform = &trim_isoform($trim_coords_aref, $isoform);
my $new_cdna_len = $isoform->get_cDNA_length();
print "\nLengths, before: $cdna_len, targeted: $targeted_cdna_len, now: $new_cdna_len\n" if $DEBUG;
print "\nAfter: (trimmed cdna length: " . join("-", @$trim_coords_aref) . " of len $cdna_len\n" if $DEBUG;
print "# $isoform_acc trimmed from $cdna_len to $new_cdna_len cdna length\n";
$trimmed_flag = 1;
}
}
}
if ($trimmed_flag) {
$gene_obj_ref->refine_gene_object();
}
print $gene_obj_ref->to_GFF3_format() . "\n";
}
}
exit(0);
####
sub trim_isoform {
my ($trim_coords_aref, $isoform) = @_;
my ($trim_end5, $trim_end3) = @$trim_coords_aref;
my $cdna_length = 0;
my $orient = $isoform->get_orientation();
my @exons = $isoform->get_exons();
@exons = sort {$a->{end5}<=>$b->{end3}} @exons;
my @coordsets;
for (my $i = 0; $i <= $#exons; $i++) {
my $exon = $exons[$i];
my ($end5, $end3) = $exon->get_coords();
my ($lend, $rend) = sort {$a<=>$b} ($end5, $end3);
$cdna_length += $rend - $lend + 1;
if (my $cds = $exon->get_CDS_obj()) {
my ($cds_end5, $cds_end3) = $cds->get_coords();
my ($cds_lend, $cds_rend) = sort {$a<=>$b} ($cds_end5, $cds_end3);
push (@coordsets, [ [$lend,$rend], [$cds_lend,$cds_rend] ]);
}
else {
push (@coordsets, [ [$lend,$rend], [] ]);
}
}
my ($trim_lend, $trim_rend) = ($trim_end5, $trim_end3);
if ($orient eq '-') {
$trim_lend = $cdna_length - $trim_lend + 1;
$trim_rend = $cdna_length - $trim_rend + 1;
($trim_lend, $trim_rend) = ($trim_rend, $trim_lend);
}
if ($DEBUG) {
print Dumper(\@coordsets);
print "Trimming coordinates: $trim_lend - $trim_rend\n";
}
## do trimming.
my @new_coordsets;
my $cdna_lend_length = 0;
foreach my $coordset (@coordsets) {
my ($exon_coordset, $cds_coordset) = @$coordset;
my ($exon_lend, $exon_rend) = @$exon_coordset;
my ($cds_lend, $cds_rend) = @$cds_coordset;
my ($original_exon_lend, $original_exon_rend) = ($exon_lend, $exon_rend);
my $exon_len = $exon_rend - $exon_lend + 1;
## checking Left end:
{
if ((! $cds_lend) && $exon_len + $cdna_lend_length < $trim_lend) {
# utr exon trimmed off
# erase
($exon_lend, $exon_rend) = (undef, undef);
}
elsif ($trim_lend > $cdna_lend_length && $trim_lend <= $cdna_lend_length + $exon_len) {
## trim point within exon
my $delta = $trim_lend - $cdna_lend_length;
my $new_exon_lend = $exon_lend + $delta - 1;
$exon_lend = $new_exon_lend;
if ($cds_lend && $exon_lend > $cds_lend) {
$exon_lend = $cds_lend; # just erasing the left utr
}
}
}
## checking right end
if ($exon_lend) {
if ( (! $cds_lend) && $trim_rend < $cdna_lend_length) {
# trim point is before utr exon
# erase it
($exon_lend, $exon_rend) = (undef, undef);
}
elsif ($trim_rend > $cdna_lend_length && $trim_rend <= $cdna_lend_length + $exon_len) {
my $delta = $trim_rend - $cdna_lend_length;
my $new_exon_rend = $original_exon_lend + $delta - 1;
$exon_rend = $new_exon_rend;
if ($cds_lend && $exon_rend < $cds_rend) {
# just removing right utr
$exon_rend = $cds_rend;
}
}
}
push (@new_coordsets, [ [$exon_lend, $exon_rend], [$cds_lend, $cds_rend] ]);
$cdna_lend_length += $exon_len;
}
## update gene object coordinates.
my %exon_coords;
my %cds_coords;
foreach my $new_coordset (@new_coordsets) {
my ($exon_coords_aref, $cds_coords_aref) = @$new_coordset;
my ($exon_lend, $exon_rend) = @$exon_coords_aref;
my ($cds_lend, $cds_rend) = @$cds_coords_aref;
if ($exon_lend) {
my ($exon_end5, $exon_end3) = ($orient eq '+') ? ($exon_lend, $exon_rend) : ($exon_rend, $exon_lend);
$exon_coords{$exon_end5} = $exon_end3;
}
if ($cds_lend) {
my ($cds_end5, $cds_end3) = ($orient eq '+') ? ($cds_lend, $cds_rend) : ($cds_rend, $cds_lend);
$cds_coords{$cds_end5} = $cds_end3;
}
}
$isoform->populate_gene_obj(\%cds_coords, \%exon_coords);
return($isoform);
}
|
