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|
#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use GFF3_alignment_utils;
use WigParser;
use Data::Dumper;
my $usage = "usage: $0 gmap.gff3 jaccard.wig [lowest_in_window_size=300]\n\n";
my $gmap_gff3 = $ARGV[0] or die $usage;
my $jaccard_wig = $ARGV[1] or die $usage;
my $window_search = $ARGV[2] || 300;
main: {
print STDERR "-indexing wig: $jaccard_wig\n";
my $wig_parser = new WigParser($jaccard_wig);
my $alignment_indexer_href = {};
print STDERR "-parsing GFF3 file: $gmap_gff3\n";
my %contig_to_alignment_ids = &GFF3_alignment_utils::index_GFF3_alignment_objs($gmap_gff3, $alignment_indexer_href);
## group multi-paths
my %core_acc_to_alignments;
print STDERR "-grouping alignments by acc.\n\n";
foreach my $contig (keys %contig_to_alignment_ids) {
my @align_ids = @{$contig_to_alignment_ids{$contig}};
foreach my $align_id (@align_ids) {
my $core_acc = $align_id;
$core_acc =~ s/\.path\d+$//;
push (@{$core_acc_to_alignments{$core_acc}}, $align_id);
}
}
print STDERR "-examining chimeras.\n";
foreach my $core_acc (keys %core_acc_to_alignments) {
my @align_ids = @{$core_acc_to_alignments{$core_acc}};
my $num_alignments = scalar(@align_ids);
if ($num_alignments != 2) {
next;
}
#print "Got: " . join(", ", @align_ids) . "\n";
my @alignment_objs;
my @mcoordsets;
my @genome_map_entries;
foreach my $align_id (@align_ids) {
my $align_obj = $alignment_indexer_href->{$align_id} or die "Error, no alignment retrieved for $align_id";
push (@alignment_objs, $align_obj);
my @trans_coords = $align_obj->get_mcoords();
my ($trans_left, $trans_right) = sort {$a<=>$b} @trans_coords;
push (@mcoordsets, [$trans_left, $trans_right]);
my $genome_acc = $align_obj->{genome_acc};
my ($genome_lend, $genome_rend) = $align_obj->get_coords;
push (@genome_map_entries, {
genome_acc => $genome_acc,
genome_lend => $genome_lend,
genome_rend => $genome_rend,
trans_lend => $trans_coords[0],
trans_rend => $trans_coords[1],
} );
}
@mcoordsets = sort {$a->[0]<=>$b->[0]} @mcoordsets;
#print "// $core_acc\n" . Dumper(\@mcoordsets) . "\n";
my $clip_pt = $mcoordsets[0]->[1];
my $wig_val = -1;
my $num_single = -1;
my $num_both = -1;
eval {
my @wig_array = $wig_parser->get_wig_array($core_acc, 1);
if ($#wig_array > $clip_pt) {
$wig_val = &find_lowest_in_window(\@wig_array, $clip_pt, $window_search); #$wig_array[$clip_pt];
}
if (! defined $wig_val) {
$wig_val = -1;
}
if (ref $wig_val) {
$num_single = $wig_val->[1];
$num_both = $wig_val->[2];
$wig_val = $wig_val->[0];
}
};
if ($@) {
print STDERR "No jaccard wig pt for $core_acc\n";
}
@genome_map_entries = sort {$a->{trans_lend}<=>$b->{trans_lend}} @genome_map_entries;
my $out_text = join("\t", $core_acc, $clip_pt, $wig_val, $num_single, $num_both);
foreach my $map_entry (@genome_map_entries) {
$out_text .= "\t" . $map_entry->{genome_acc} . ":"
. $map_entry->{genome_lend} . "(" . $map_entry->{trans_lend} . ")"
. "-"
. $map_entry->{genome_rend} . "(" . $map_entry->{trans_rend} . ")";
}
print $out_text . "\n";
}
exit(0);
}
####
sub find_lowest_in_window {
my ($wig_array_aref, $clip_pt, $window_search) = @_;
my $left_search = int($clip_pt - ($window_search/2));
if ($left_search < 1) { $left_search = 1; }
my $right_search = int($clip_pt + ($window_search/2));
if ($right_search > $#$wig_array_aref) {
$right_search = $#$wig_array_aref;
}
my $wig_chosen;
for (my $i = $left_search; $i <= $right_search; $i++) {
my $wig_ref = $wig_array_aref->[$i];
if (ref $wig_ref) {
if ( (! defined $wig_chosen)
||
$wig_ref->[0] < $wig_chosen->[0]
||
($wig_ref->[0] == $wig_chosen->[0] && $wig_ref->[2] > $wig_chosen->[2]) ) {
$wig_chosen = $wig_ref;
}
}
}
return($wig_chosen);
}
|
