classify_link.pl

use strict;
use warnings;
use AlignDB::IntSpan;

open CP,"<",$ARGV[0];
open CR,"<",$ARGV[1];
open BR,"<",$ARGV[2];
open TC,"<",$ARGV[3];
open ACR,">",$ARGV[4];
open ABR,">",$ARGV[5];
open ATC,">",$ARGV[6];
open BTC,">",$ARGV[7];

my $fm = $ARGV[8];
my $fz = $ARGV[9];

my @cr = <CR>;
my @br = <BR>;
my @tc = <TC>;

close CR;
close BR;
close TC;

my @mcx_cr;
my @mcx_br;
my @mcx_tc;

foreach(1..5){
	chomp($cr[$_]);
	chomp($br[$_]);
	chomp($tc[$_]);
	my @tmp_cr = split(": ",$cr[$_]);
	my @tmp_br = split(": ",$br[$_]);
	my @tmp_tc = split(": ",$tc[$_]);

	$mcx_cr[$_] = AlignDB::IntSpan->new;
	$mcx_br[$_] = AlignDB::IntSpan->new;
	$mcx_tc[$_] = AlignDB::IntSpan->new;

	$mcx_cr[$_]->add_runlist($tmp_cr[1]);
	$mcx_br[$_]->add_runlist($tmp_br[1]);
	$mcx_tc[$_]->add_runlist($tmp_tc[1]);
}

my %cov = ('I'=>1,'II'=>2,'III'=>3,'IV'=>4,'V'=>5);

while(<CP>){
	chomp;
	my @tmp = split(" ",$_);
	my $set1 = AlignDB::IntSpan->new;
	my $set2 = AlignDB::IntSpan->new;
	my $out1;
	my $out2;
	if($tmp[1]<$tmp[2]){
		$out1 = $tmp[0]." ".$tmp[1]." ".$tmp[2];
		$set1->add_pair($tmp[1],$tmp[2]);
	}else{
		$out1 = $tmp[0]." ".$tmp[2]." ".$tmp[1];
		$set1->add_pair($tmp[2],$tmp[1]);
	}

	if($tmp[4]<$tmp[5]){
		$out2 = $tmp[3]." ".$tmp[4]." ".$tmp[5];
		$set2->add_pair($tmp[4],$tmp[5]);
	}else{
		$out2 = $tmp[3]." ".$tmp[5]." ".$tmp[4];
		$set2->add_pair($tmp[5],$tmp[4]);
	}

	my $cr_comp;
	if(($fm * $set1->overlap($mcx_cr[$cov{$tmp[0]}]) >= $fz * $set1->size) and ($fm * $set2->overlap($mcx_cr[$cov{$tmp[3]}]) >= $fz * $set2->size)){
		$cr_comp = 3;
	}elsif($fm * $set2->overlap($mcx_cr[$cov{$tmp[3]}]) >= $fz * $set2->size){
		$cr_comp = 2;
	}elsif($fm * $set1->overlap($mcx_cr[$cov{$tmp[0]}]) >= $fz * $set1->size){
		$cr_comp = 1;
	}else{
		$cr_comp = 0;
	}
	my $br_comp;
	if(($fm * $set1->overlap($mcx_br[$cov{$tmp[0]}]) >= $fz * $set1->size) and ($fm * $set2->overlap($mcx_br[$cov{$tmp[3]}]) >= $fz * $set2->size)){
		$br_comp = 3;
	}elsif($fm * $set2->overlap($mcx_br[$cov{$tmp[3]}]) >= $fz * $set2->size){
		$br_comp = 2;
	}elsif($fm * $set1->overlap($mcx_br[$cov{$tmp[0]}]) >= $fz * $set1->size){
		$br_comp = 1;
	}else{
		$br_comp = 0;
	}
	my $tc_comp;
	if(($fm * $set1->overlap($mcx_tc[$cov{$tmp[0]}]) >= $fz * $set1->size) and ($fm * $set2->overlap($mcx_tc[$cov{$tmp[3]}]) >= $fz * $set2->size)){
		$tc_comp = 3;
	}elsif($fm * $set2->overlap($mcx_tc[$cov{$tmp[3]}]) >= $fz * $set2->size){
		$tc_comp = 2;
	}elsif($fm * $set1->overlap($mcx_tc[$cov{$tmp[0]}]) >= $fz * $set1->size){
		$tc_comp = 1;
	}else{
		$tc_comp = 0;
	}

	if(($cr_comp==1) and ($br_comp==1) and ($tc_comp==1)){
		print ACR "$out1 $out2\n";
	}elsif(($cr_comp==2) and ($br_comp==2) and ($tc_comp==2)){
		print ACR "$out2 $out1\n";
	}elsif(($cr_comp==3) and (($br_comp==1) and ($tc_comp==1))){
		print ABR "$out1 $out2\n";
	}elsif(($cr_comp==3) and (($br_comp==2) and ($tc_comp==2))){
		print ABR "$out2 $out1\n";
	}elsif(($cr_comp==3) and ($br_comp==3) and ($tc_comp==1)){
		print ATC "$out1 $out2\n";
	}elsif(($cr_comp==3) and ($br_comp==3) and ($tc_comp==2)){
		print ATC "$out2 $out1\n";
	}elsif(($cr_comp==3) and ($br_comp==3) and ($tc_comp==3)){
		print BTC "$out1 $out2\n";
	}
}
close CP;
close ACR;
close ABR;
close ATC;
close BTC;