Get the last 10 elements of the array:

@array = qw /1 2 3 4 5 6 7 8 9 10 11 12 13 14 15/;
print join ' ', @array[-10 .. -1];
[download]

That was my original approach in returning the 'right' side. I found the approach I ended up taking a bit more readable and intuitive.


--
"Language shapes the way we think, and determines what we can think about."
-- B. L. Whorf

use strict;
use warnings;

my $fh;
open $fh, '<', 'file2.txt' or die "cant open file2.txt: $!";
my %info;
while (<$fh>) {
    if (/^>(.*)_left\s\w+=(\d+)/) {
        $info{$1}{left} = $2;
    }
    if (/^>(.*)_right\s\w+=(\d+)/) {
        $info{$1}{right} = $2;
    }
}
close $fh;

# comparing with file 1
open $fh, '<', 'file1.txt' or die "cant open file1.txt: $!";
my $id;
while (<$fh>) {
    if (/^>(\w+)/) {
        $id = $1;
    }
    else {
        my @nums = split;
        my $len  = $info{$id}{left};
        print ">${id}_left length=$len\n";
        print "@nums[0..($len-1)]\n"; 
        $len = $info{$id}{right};
        print ">${id}_right length=$len\n";
        print "@nums[($#nums-$len)..$#nums]\n"; 
    }

}

__END__
>AAAT3R_left length=6
40 40 40 40 40 40
>AAAT3R_right length=62
40 40 40 40 40 40 38 38 37 39 36 36 40 36 35 35 35 38 40 35 35 33 35 3
+5 35 40 40 40 40 37 37 38 38 38 40 40 40 40 40 40 40 40 40 40 40 40 4
+0 40 40 40 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 37 33 32 32 30 20 17 17 17 0
[download]

That was a lot of code to try to get what you wanted. I used a (to me) simpler approach:

1. Read in file1
   1. Looping through the file
      1. If a blank line or only contains whitespace, skip
      2. If the line begins with a '>', split on whitespace to get the sequence name
      3. Otherwise, split the line on whitespace into an array in a hash, keyed by the sequence name
2. Read in file2
   1. Looping through the file
      1. If a blank line or only contains whitespace, skip
         1. If the line begins with a '>'
         2. Split the line on understore, equal, or whitespace to get the sequence name, "side", and length
         3. If the sequence is not defined, display a warning
         4. Generate the range based on the "side"
         5. Print the line
         6. Print the digit sequence range
      2. Otherwise, display the line

Or, in code:

Hope that helps.

If I understand the problem correctly, then you might try approaching it like this:

#!/usr/bin/perl -w
use strict;

our ($File1, $File2) = qw/file1 file2/;
open File1 or die "$File1: $!\n";
open File2 or die "$File2: $!\n";

my ($key, %results);
while (<File1>){
    next if /^\s*$/;
    chomp;
    if (/^>\s*(\S+)/){
        $key = $1;
    }
    else {
        $results{$key} = [ split ];
    }
}
close File1;

my ($len, $side, $str);
while (<File2>){
    next if /^\s*$/;
    if (/^>([^_]+)_(left|right).*?(\d+)\s*$/){
        print;
        $str = $1;
        $side = $2;
        $len = $3;
    }
    else {
        my @list;
        @list = @{$results{$str}};
        if ($side eq 'left'){
            die "$str is too short for a left slice of $len!\n"
                unless @list >= $len;
            print "@list[0..$len-1]\n";
        }
        else {
            die "$str is too short for a right slice of $len!\n"
                unless @list >= $len;
            print "@list[@list-$len..$#list]\n";
        }
    }
}
close File2;
[download]

open(FILE1,"file1.txt") or die $!;@file1=<FILE1>;close(FILE1);
open(FILE2,"file2.txt") or die $!;@file2=<FILE2>;close(FILE2);
foreach $file2(@file2){
        if($file2=~/(\w+)(_)(\w+)\s(\w+)(=)(\d+)/)
        {
                $id=$1;
                if($3 eq 'right'){$value=$6."r#";}
                if($3 eq 'left'){$value=$6."l";}
                push(@array,"$value");  push(@id,"$id");
        }
}
push(@newid,grep {!$ss{$_}++} @id);
@arraysplit=@array2=$ss=();
$ss=join('',@array); @arraysplit=split(/\s+|\n/,$ss);
@array2=split('#',$arraysplit[0]);
foreach $f1(0 .. $file1[$#fiel1])
{
        if($file1[$f1] =~/>/){  $firstline=$file1[$f1]; chomp($firstli
+ne);      }
        if($file1[$f1] =~/^>/)
        {
                $secondline=$file1[$f1+1];
                $secondlinej=join('',split(/\n/,$secondline));
                foreach $vv(0 .. scalar @array2)
                {
                        if($newid[$vv] eq substr($firstline,1,6))
                        {
                                ($left,$right)=split(/r|l/,$array2[$vv
+]);
                                print "\n".substr($firstline,0,7)."_le
+ft"." length=$left  \n";
                                @secondlinejj=split('\s',$secondlinej)
+;
                                for ($l=0;$l < $left;$l++){print "$sec
+ondlinejj[$l] ";}  print "\n";
                                print "\n".substr($firstline,0,7)."_ri
+ght"." length=$right \n";
                                $len=scalar @secondlinejj."\n";
                                $right=$len-$right;
                                for ($m=$right;$m <= scalar @secondlin
+ejj;$m++){print "$secondlinejj[$m] ";}print "\n"
                        }
                }
        }
}
[download]

>AAAT3R_left length=6
40 40 40 40 40 40

>AAAT3R_right length=62
40 40 40 40 40 38 38 37 39 36 36 40 36 35 35 35 38 40 35 35 33 35 35 3
+5 40 40 40 40 37 37 38 38 38 40 40 40 40 40 40 40 40 40 40 40 40 40 4
+0 40 40 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 3737 33 32 32 30 20 17 17 17 0
[download]