#!/usr/bin/perl use strict; #processing file2 open(FH1,"file2.txt") or die "cant open"; my @ar=; my $left;my $right;my @final; foreach my $aray(@ar){ if($aray=~m/left/){ if($aray=~m/(^>.*)_\w+\s\w+(=)(\d+)/){ $left=$3; } } else{ my $right_header=$aray; if($aray=~m/(^>.*)_\w+\s\w+(=)(\d+)/){ $right=$3; push(@final,$1); push(@final,"left=$left".".."."right=$right"); } } } my %hash=@final; my $val;my $head; my ($leftnew,$rightnew);my ($side1,$num1);my ($side2,$num2); my @numright;my @numleft;my @string;my @string1; #comparing with file 1 open(FH2,"file1.txt") or die "cant open"; my @ar2=; my $aray2; while (my ($key,$value)=each %hash){ foreach $aray2(@ar2){ if ($aray2=~m/^(>\w+)/){ $head=$1; } $val=$hash{$key}; ($leftnew,$rightnew)=split(/\../,$val); ($side1,$num1)=split(/=/,$leftnew); ($side2,$num2)=split(/=/,$rightnew); @numleft=split(' ',$aray2); @numright=reverse(@numleft); if ($head eq $key){ if($aray2=~m/^\d+/){ my $i;my $j; for($i=0;$i