coding:  
  

    use Getopt::Long qw(:config no_ignore_case);
    use Data::Dumper;
    use POSIX qw(floor);
    use strict;
    use warning;
    
    my $orig = '';
    my $new = '';
    
    GetOptions('orig=s' => \$orig, 'new=s' => \$new);
    
    if (!$orig|!$new) {
            print "\n\t Help: test.pl -orig <file A> -new <file B>\n";
            exit;
    }
    
    open (PASS, ">pass.rpt") || die "ERROR: cannot open";
    open (FAIL, ">fail.rpt") || die "ERROR: cannot open";
    open (NC, ">noCheck.rpt") || die "ERROR: cannot open";
    open (t1, ">t1") || die "ERROR: cannot open";
    open (t2, ">t2") || die "ERROR: cannot open";
    
    my (@array, $line, $end1, $slack1, $b1, $THIS, @arr1, @arr2, @tmp1, @tmp2, @emp, @emp2, $data1, $data2,$emp1,$emp2,$emp3,$emp4,$ep1,$s1,$ep2,$s2,$ncc,$pc,$fc);
    
    $ncc = 0;
    $pc = 0;
    $fc = 0;
    
    fileA_ext();
    fileB_ext();
    check();
    
    #_______________________________________________________________________________________________ 
    sub fileA_ext() {
    
    if ($orig =~ /\S+\.gz$/) {
       open (FileA,"gunzip -c $orig |") || die "ERROR: can't read $orig\n";
    } else {
       open (FileA,"$orig") || die "ERROR: can't read $orig\n";
    }
    
    while (@array = <FileA>)	{
    
    foreach $line(@array) {
    
            if ($line =~ m/(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)/) {
    
    
    		if ($line !~ m/\((sa)\)/) {
    
    			@arr1 = @emp;
    			next if ($line =~ m/Name/);
                    	$name1 = "$1";
    			$score1 = "$12";
    				
    			my $data1 = join(";",$name1,$score1);	 
    			push (@arr1, $data1);
    			
    			}
    		
    		if ($line =~ m/\((sa)\)/) {
    
    			@arr1 = @emp2;
    			@tmp1 = @emp;
    			next if ($line =~ m/Name/);
    			push (@tmp1, $line);
    			#print t "@tmp1\n";
    
    			foreach $line (@tmp1) {
    				
    				if ($line =~ m/(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)/) {
    
    					my $name2 = "$1";
    					substr($name2, -13) = '';
    					my $score2 = "$12";
    
    					my $data1 = join(";",$name2,$score2);	 
    					push (@arr1, $data1);
    					$name2 = $score2 ="";
    					#print "@arr1\n\n";
    								}
    							}
    						}
    print t1 "@arr1\n\n";
    }        
    }
    }
    close (FileA);
    }
    
    #____________________________________________________________________________________________
    
                           
    sub FileB_ext() {
    
    if ($new =~ /\S+\.gz$/) {
       open (FileB,"gunzip -c $new |") || die "ERROR: $THIS can't read $new\n";
    } else {
       open (FileB,"$new") || die "ERROR: $THIS can't read $new\n";
    }
    
    while (@array = <FileB>)  {
    
    foreach $line(@array) {
    
         if ($line =~ m/(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)/) {
    		#print "$line\n";
    
    		if ($line !~ m/\((sa)\)/) {
    
    			@arr2 = @emp;
    			next if ($line =~ m/Name/);
                    	my $name3 = "$1";
    			my $score3 = "$12";
    				
    			my $data2 = join(";",$name3,$score3);	 
    			push (@arr2, $data2);
    			
    			}
    		
    		if ($line =~ m/\((sa)\)/) {
    
    			@arr2 = @emp2;
    			@tmp2 = @emp;
    			next if ($line =~ m/Name/);
    			push (@tmp2, $line);
    			#print t "@tmp2\n";
    
    			foreach $line (@tmp2) {
    				
    				if ($line =~ m/(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)\s+(.*)/) {
    
    					my $name4 = "$1";
    					substr($name4, -13) = '';
    					my $score4 = "$12";
    
    					my $data2 = join(";",$name4,$score4);	 
    					push (@arr2, $data2);
    					$name4 = $score4 ="";
    					#print "@arr2\n\n";
    								}
    							}
    						}
    print t2 "@arr2\n\n";
    }         
    }
    }
    close (FileB);
    }
    
    
    sub check() {
    
    foreach $data1 (@arr1) {
    	if ($data1 ne ""){
    
    		if ($data1 =~ m/(.*)\;(.*)/) {
    			$ep1 = $emp1;
    			$s1 = $emp2;
    			my $ep1 = "$1";
    			my $s1 = "$2";
    			#print r "$ep1  $s1\n\n";
    	
    		foreach $data2 (@arr2) {
    			if ($data2 ne "") {
    
    				if ($data2 =~ m/(.*)\;(.*)/) {
    					$ep2 = $emp3;
    					$s2 = $emp4;
    					my $ep2 = "$1";
    					my $s2 = "$2";
    					#print R "$ep2 $s2\n";
    						
    
    				if ( $ep1 eq $ep2 && $s1 =~ m/-/g) {
    					
    					$ncc++;
    					#print NC "Total match: $ncc\n\n";
    					print NC "$ep1	$s1	$s2\n";
    									}
    
    				if ( $ep1 eq $ep2 && $s1 !~ m/-/g && $s1 > 50 && $s2 > 40) {
    
    					$pc++;
    					print PASS "$ep1	$s1	$s2\n";
    										}
    
    				if ( $ep1 eq $ep2 && $s1 !~ m/-/g && $s1 < 50 && $s2 < 40) {
    
    					$fc++;
    					print FAIL "$ep1	$s1	$s2\n";
    										}
    
    
    }
    }
    }
    }
    }
    }
    print NC "\nTotal match: $ncc\n\n";
    print PASS "\nTotal match: $pc\n\n";
    print FAIL "\nTotal match: $fc\n\n";
    
    
    }