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#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 fileA.maps fileB.maps gene_annots.gff3\n\n";
my $file_A_maps = $ARGV[0] or die $usage;
my $file_B_maps = $ARGV[1] or die $usage;
my $gene_annots_gff3 = $ARGV[2] or die $usage;
main: {
my ($A_fusion_to_genes_href, $A_FL_genes) = &parse_map_file($file_A_maps);
my ($B_fusion_to_genes_href, $B_FL_genes) = &parse_map_file($file_B_maps);
my %gene_structs = &get_gene_positions($gene_annots_gff3);
my %all_fusions = map { $_ => 1 } (keys %$A_fusion_to_genes_href, keys %$B_fusion_to_genes_href);
foreach my $fusion (keys %all_fusions) {
my $neighboring = &are_neighboring($fusion, \%gene_structs);
print "$fusion\t$neighboring\t";
if ($A_fusion_to_genes_href->{$fusion} && $B_fusion_to_genes_href->{$fusion}) {
print "BOTH\n";
}
elsif ($A_fusion_to_genes_href->{$fusion}) {
print "A_only\n";
}
elsif ($B_fusion_to_genes_href->{$fusion}) {
print "B_only\n";
}
}
exit(0);
}
####
sub parse_map_file {
my ($map_file) = @_;
my %fusion_to_genes;
my %FL_genes;
open (my $fh, $map_file) or die $!;
while (<$fh>) {
chomp;
my ($fl_entries, $rest) = split(/\t/);
my @genes = split(/,/, $fl_entries);
foreach my $gene (@genes) {
$FL_genes{$gene} = $fl_entries;
}
if (scalar @genes > 1) {
$fusion_to_genes{$fl_entries} = \@genes;
}
}
close $fh;
return(\%fusion_to_genes, \%FL_genes);
}
####
sub get_gene_positions {
my ($annot_file) = @_;
my %gene_structs;
my %scaff_to_structs;
open (my $fh, $annot_file) or die $!;
while (<$fh>) {
chomp;
unless (/\w/) { next; }
my @x = split(/\t/);
if ($x[2] eq 'gene') {
$x[8] =~ /ID=([^;]+)/ or die "Error, cannot parse ID from $x[8]";
my $gene_id = $1;
my $struct = { scaffold => $x[0],
midpt => ($x[3]+$x[4])/2,
order => undef,
gene_id => $gene_id,
};
$gene_structs{$gene_id} = $struct;
push (@{$scaff_to_structs{$x[0]}}, $struct);
}
}
close $fh;
## order the genes.
my $pos = 0;
foreach my $scaff (keys %scaff_to_structs) {
my @structs = @{$scaff_to_structs{$scaff}};
@structs = sort {$a->{midpt}<=>$b->{midpt}} @structs;
foreach my $struct (@structs) {
$pos++;
$struct->{order} = $pos;
}
$pos++; # gap between scaffs
}
return(%gene_structs);
}
####
sub are_neighboring {
my ($fusion, $gene_structs_href) = @_;
my @gene_structs;
foreach my $gene (split(/,/, $fusion)) {
my ($trans_id, $gene_id) = split(/;/, $gene);
my $gene_struct = $gene_structs_href->{$gene_id} or die "Error, no gene struct for $gene_id";
push (@gene_structs, $gene_struct);
}
@gene_structs = sort {$a->{order}<=>$b->{order}} @gene_structs;
if ($gene_structs[1]->{order} - $gene_structs[0]->{order} <= 4 ) {
return("Neighbors");
}
else {
return("NOT_neighbors ($gene_structs[0]->{order} vs. $gene_structs[1]->{order})");
}
}
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