#!/usr/bin/perl

open(FILE, "$ARGV[0]")|| die "Can not open $ARGV[0]!!\n";
#open(OUT, ">>$ARGV[1]")|| die "Can not open $ARGV[1]!!\n";
%id = ();
#$org = lc($ARGV[1]); 
#print "Organism: $org"; 

while(<FILE>){
	chomp($_);
	my @field = split(" ", $_);
	#if($org eq "human"){
	$hs = &align_hs($field[0]);
	#}
	#elsif($org eq "rat"){
	$rn = &align_rn($field[4]);
	#}
	#elsif($org eq ""){
	$bt = &align_bt($field[1]);
	#}
	#elsif($org eq "mouse"){
	$mm = &align_mm($field[3]);
	#}
	#elsif($org eq "dog"){
	$cf = &align_cf($field[2]);
	#}
	print "#$_\n$hs\n$bt\n$cf\n$mm\n$rn\n\n";
}


sub align_hs {
	my $field = shift(@_);
	my @char = split("-", $field);
	#print $char[0],"\t$char[1]\n";
	my $find = $char[0]." ".$char[1];
	#print "$find\n";
	my $intron = `grep -A 1 --p "$find" $ARGV[1]`;
	return $intron;
}

sub align_rn {
        my $field = shift(@_);
        my @char = split("-", $field);
        #print $char[0],"\t$char[1]\n";
	my $find = $char[0]." ".$char[1];
        #print "$find\n";
        my $intron = `grep -A 1 --p "$find" $ARGV[5]`;
        return $intron;
}

sub align_bt {
        my $field = shift(@_);
        my @char = split("-", $field);
        #print $char[0],"\t$char[1]\n";
	my $find = $char[0]." ".$char[1];
        #print "$find\n";
        my $intron = `grep -A 1 --p "$find" $ARGV[2]`;
        return $intron;
}

sub align_mm {
        my $field = shift(@_);
        my @char = split("-", $field);
        #print $char[0],"\t$char[1]\n";
	my $find = $char[0]." ".$char[1];
        #print "$find\n";
        my $intron = `grep -A 1 --p "$find" $ARGV[4]`;
        return $intron;
}

sub align_cf {
        my $field = shift(@_);
        my @char = split("-", $field);
        #print $char[0],"\t$char[1]\n";
        my $find = $char[0]." ".$char[1];
        #print "$find\n";
        my $intron = `grep -A 1 --p "$find" $ARGV[3]`;
	return $intron;
}