Dear monks, With reference to the query "sorting and other problems in hash" posted by me last week, i have several doubts. As per the corrections given by you all, and after thoroughly understanding each and every line of the code, i tried to solve the problem. Ofcourse i did get the results only for the sample file and not for the original file. The reason being that the original file is 8GB in size, i doubt if this is the right approach. Just to load the file and count the lines in it using a while, it takes 1 minute. Then why is the following program takes forever, but not print the output at all? Please help me solve this problem. I need to process the 8 gig of data by any means :( 
#!/usr/bin/perl

use strict;
use warnings;

if ( scalar @ARGV < 2 ) {
    die("Usage:\n\t$0 file1 file2\n\n");
}

my %data;

my $fn = $ARGV[0];
{
    my $sequence;
    open DF, $fn or die $!;
    while ( my $line = <DF> ) {
        chomp $line;
        next if $line =~ m/^\s*$/;
        if ( substr( $line, 0, 1 ) eq '>' ) {
            ( $sequence, undef ) = split /\s+/, $line;
        }
        else {
            @{ $data{$sequence} } = split /\s+/, $line;
        }
    }
    close DF;
}

$fn = $ARGV[1];
{
    my $sequence;
    my $side;
    my $len;
    open DF, $fn or die $!;
    while ( my $line = <DF> ) {
        chomp $line;
        next if $line =~ m/^\s*$/;

        if ( substr( $line, 0, 1 ) eq '>' ) {
            ( $sequence, $side, undef, $len ) =
              split /(?:_|=|\s)+/, $line;
            if ( defined @{ $data{$sequence} } ) {
                my @range = ( 0, $len - 1 );
                if ( $side ne "left" ) {
                    @range = ( -1 * $len, -1 );
                }
                print $line, "\n";
                print join( ' ',
                    @{ $data{$sequence} }
                      [ $range[0] .. $range[1] ] ),
                  "\n";
            }
            else {
                warn "No data read from "
                  . $ARGV[0]
                  . " for sequence $sequence\n";
            }
        }
        else {
            print join( "  ", split //, $line ), "\n";
        }
    }
    close DF;
}

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In reply to When the input file is huge !!! by sugar

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