# This is part of the parser to find protein ID mapping with equal sequences

while(<In_Query>){
	chomp;	
	if(/^> (.*)/){
	  $query{$1} = "" ;
	}
	else{
		$query{$1} = $query{$1}.$_ ;
	}
}
close In_Query;

while(<In_Subject>){
	chomp;	
	if(/^> (.*)/){
	  $subject{$1} = "" ;
	}
	else{
		$subject{$1} = $subject{$1}.$_ ;
	}
}
close In_Subject;

foreach $tmp (keys (%query) ){
	if( !exists($seq2query{$query{$tmp}}) ){
		$seq2query{$query{$tmp}} = $tmp ;
	}
	else{
		$seq2query{$query{$tmp}} = $seq2query{$query{$tmp}}.";".$tmp ;
	}
}




foreach $tmp (keys (%subject) ){
	if( exists($seq2query{$subject{$tmp}}) ){
		$equal1{$subject{$tmp}} = $seq2query{$subject{$tmp}} ;
		if( !exists($equal2{$subject{$tmp}}) ){
			$equal2{$subject{$tmp}} = $tmp ;
		}
		else{
			$equal2{$subject{$tmp}} = $equal2{$subject{$tmp}}.";".$tmp ;
		}
	}
}

print Out "$queryName\t$subjectName\n" ;
foreach $tmp (keys (%equal1) ){
		print Out $equal1{$tmp}."\t".$equal2{$tmp}."\n" ;
}
close Out;