Thanks for this. Now if instead of only testing one set of $chrom,$start,$Stop I have an array of these values where Id like to test each one.

Im having a problem with exiting "while ( defined(my $line=<DATA>) and !@values)" I try to clear values but that wont work 

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

my @triples = ("chr1 9837 9840", "chr1 99998 99999", "chr2 9838 9840")
+;


my($start,$chrom,$stop);
foreach my $triple (@triples){
  print "$triple :";
  ($chrom,$start,$stop)=split(/\s+/,$triple);
  my @values=();
  while ( defined(my $line=<DATA>) and !@values)
  {
    @values = get_values() if ( $line =~ m/\=$chrom$/);
    if(@values)
    {
    print "average ", average(\@values), "\n";
    }else {print "not found: average NA \n";}
  }
}



sub get_values
{
    my @values;
    while ( defined(my $line=<DATA>)  )
    {
       last unless $line =~ m/^\d/;
       my ($tag,$value) = split(/\s+/,$line);
       push (@values, $value) if ($tag >= $start and $tag <= $stop);
    }
    return @values
}

sub average
{
    my ($array_ref) = @_;
    my $sum;
    my $count = scalar @$array_ref;
    foreach (@$array_ref) { $sum += $_; }
    return $sum / $count;
} 

__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

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In reply to Re^4: extract relevent lines according to array by coldy
in thread extract relevent lines according to array by coldy

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