You try the following script to do it. 
use strict;
use warnings;
use Data::Dumper;


my $chrom='chr1';
my $start=9839;
my $stop=9841;

my %hash=();

my @values=();

while(<DATA>)
{
        if(/[a-z]+\s*chrom=$chrom/)
        {
                while(<DATA>)
                {
                if(/([0-9]+)\s*([0-9]+\.[0-9]+)/)
                {
                        $hash{$1}=$2;
                }
                else {
                        last;
                }
                }
        }
}

for ($start .. $stop) {
push @values,$hash{$_};
}

print @values;

__DATA__
variableStep chrom=chr1
9837    0.010
9838    0.008
9839    0.007
9840    0.004
9841    0.002
9842    0.001
variableStep chrom=chr2
9837    0.090
9838    0.038
9839    0.017
9840    0.044
9841    0.052
9842    0.091

[download]

In reply to Re: extract relevent lines according to array by nvivek
in thread extract relevent lines according to array by coldy

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