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#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 splicePaths_A splicePaths_B\n\n";
my $fileA = $ARGV[0] or die $usage;
my $fileB = $ARGV[1] or die $usage;
main: {
my %combosA = &get_combos($fileA);
my %combosB = &get_combos($fileB);
my %introns_to_combos;
&index_combos_by_intron(\%combosA, \%introns_to_combos);
&index_combos_by_intron(\%combosB, \%introns_to_combos);
my %seen_intron;
foreach my $intron (keys %introns_to_combos) {
if ($seen_intron{$intron}) { next; }
my %paths;
&get_all_connected_paths($intron, \%introns_to_combos, \%seen_intron, \%paths);
my @paths_A_not_B;
my @paths_B_not_A;
my @paths_both_A_and_B;
foreach my $path (keys %paths) {
if ($combosA{$path} && $combosB{$path}) {
push (@paths_both_A_and_B, $path);
}
elsif ($combosA{$path}) {
push (@paths_A_not_B, $path);
}
elsif ($combosB{$path}) {
push (@paths_B_not_A, $path);
}
}
## filter out those that are subpaths of others.
@paths_A_not_B = &remove_subpaths(\@paths_A_not_B, [@paths_B_not_A]);
@paths_B_not_A = &remove_subpaths(\@paths_B_not_A, [@paths_A_not_B]);
print join("\t", $intron,
scalar(@paths_both_A_and_B),
scalar(@paths_A_not_B),
scalar(@paths_B_not_A)) . "\n";
}
exit(0);
}
####
sub remove_subpaths {
my ($paths_query_aref, $paths_to_examine_as_containing_subpaths_aref) = @_;
my @ok;
foreach my $path (@$paths_query_aref) {
my ($chr, $rest_path) = split(/:/, $path);
my $found_as_subpath = 0;
foreach my $other_path (@$paths_to_examine_as_containing_subpaths_aref) {
if ($other_path =~ /$rest_path/) {
$found_as_subpath = 1;
last;
}
}
if (! $found_as_subpath) {
push (@ok, $path);
}
}
return(@ok);
}
####
sub get_combos {
my ($file) = @_;
my %combos;
open (my $fh, $file) or die $!;
while (<$fh>) {
chomp;
my @x = split(/\t/);
if ($x[0] =~ /COMBO/) {
$combos{$x[1]} = 1;
}
}
close $fh;
return(%combos);
}
####
sub index_combos_by_intron {
my ($combos_href, $introns_to_combos_href) = @_;
foreach my $combo (keys %$combos_href) {
my @introns = &get_introns_from_path($combo);
foreach my $intron (@introns) {
push (@{$introns_to_combos_href->{$intron}}, $combo);
}
}
return;
}
sub get_introns_from_path {
my ($path) = @_;
my ($chr, @introns) = split(/_+/, $path);
foreach my $intron (@introns) {
$intron = "$chr$intron";
}
return(@introns);
}
sub get_all_connected_paths {
my ($intron, $introns_to_combos_href, $seen_href, $paths_href) = @_;
my @paths = @{$introns_to_combos_href->{$intron}};
$seen_href->{$intron} = 1;
foreach my $path (@paths) {
if (! exists $paths_href->{$path}) {
$paths_href->{$path} = 1;
my @introns = &get_introns_from_path($path);
foreach my $intron (@introns) {
if ($seen_href->{$intron}) { next; }
&get_all_connected_paths($intron, $introns_to_combos_href, $seen_href, $paths_href);
}
}
}
return;
}
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