dear monks, i m here with yet another problem. Hope you would guide me as you have always done !!! I am comparing 2 files, i take information of left and right values from file 2, and extract numbers at the beginning(left value) and end(right value) of every string-numbers (based on their unique ID which starts with '>') from file 1. 
file1:
>AAAT3R length=110
40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4
+0 40 40 40 40 40 40 40 40 40 40 40 40 38 38 38 38 40 40 39 40 40 40 4
+0 40 40 40 40 40 40 38 38 37 39 36 36 40 36 35 35 35 38 40 35 35 33 3
+5 35 35 40 40 40 40 37 37 38 38 38 40 40 40 40 40 40 40 40 40 40 40 4
+0 40 40 40 40 37 36 36 31 22 22 22 20 20 20 20 20 14
>AAA2OJ length=70
18 18 18 21 35 35 35 32 32 32 33 35 38 39 37 37 39 39 39 39 39 40 40 3
+9 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 3
+9 37 35 35 39 37 37 37 37 37 37 37 37 37 37 33 32 32 30 20 17 17 17 0

file2:
>AAAT3R_left length=6
TACATA
>AAAT3R_right length=62
ACTACTGATTTGATTATCTTTGATCTCTGTCGAACTAACTATATCTTAGTATGATCTTTAAT
>AAA2OJ_left length=14
TTTTGGACTATCTG
>AAA2OJ_right length=14
AGGCTGTTCTTTTN

result file:(expected)
>AAAT3R_left length=6
40 40 40 40 40 40
>AAAT3R_right length=62
40 40 40 38 38 37 39 36 36 40 36 35 35 35 38 40 35 35 33 35 35 35 40 4
+0 40 40 37 37 38 38 38 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 4
+0 37 36 36 31 22 22 22 20 20 20 20 20 14
>AAA2OJ_left length=14
18 18 18 21 35 35 35 32 32 32 33 35 38 39
>AAA2OJ_right length=14
37 37 37 37 37 33 32 32 30 20 17 17 17 0

[download]
This is the code i have written so far, to get the desired output. 
#!/usr/bin/perl
use strict;
#processing file2
open(FH1,"file2.txt") or die "cant open";
my @ar=<FH1>;
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=<FH2>;
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;$i<scalar(@numleft);$i++){
                              if($i==$num1){
                                    last;
                              }else{
                              push(@string1,$numleft[$i]);
                              }
                        }
                       for ($j=0;$j<scalar(@numright);$j++){
                        if($j==$num2){
                                    last;
                              }
                              else{
                            push(@string,$numright[$j]." ");
                              }
                        }
                  }
            }
           
           
      }
      print "\n",$head.'_'.'left '.'length='.$num1,"\n";   
      print "@string1\n";
      print "\n",$head.'_'.'right '.'length='.$num2,"\n";  
      print reverse(@string),"\n";
      $key=();$value=();$aray2=();@string=();@string1=();
}

[download]
My problem here is, i am not able to print the unique header ID for every line. I know that the $string is a scalar variable and outside the loop, it will hold the last value. But dont know how to solve the problem. moreover, Want the results sorted according to the input file order. (as given in the expected result file). Please help me solve it. Thank u :)

In reply to sorting and other problems in hash by sugar

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