Hi, i really need your help. I have one file containing a long string of DNA, and another file containing the start and stop positions of genes in the DNA. like this : 
1  1800
1900 2254

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etc. in which the first number is the start position and the second is the stop position. I need to map these positions to the DNA string and replace them with X's. I dont know whether I should be treating the start/stop positons file as a hash or array?? - there are lots of values so i couldn't declare them if i used a hash. Error messages say that $finish isn't declared within the second foreach loop. Heres the code so far: 
#! /usr/local/bin/perl -w

use strict;

open (INPUT, "<positions.input") or die "unable to open file";

open (INPUT2, "<dna.file") or die "unable to open file";

open (OUTFILE, ">$$.output");

@dna = <INPUT2>;

$dna = join ('', @dna);

$dna =~ s/\s//g;

@dna = split ('', $dna);

$count = 0;

$base = ("A"| "C"| "G" | "T");

foreach $base (@dna)
{
++$count;
}


while (<INPUT>)
{
    $line = $_;
    chomp ($line);
    @orfs = ();
    @orfs = split (/\s+/, $line);

my @start = $orfs[0];
my @finish = $orfs[1];

}

foreach $start (@orfs)
{
$start = substr ($dna, 0, $start);

substr ($dna, $start +1, $finish - $start) =~ s/A-Z/X/g;
$dna =~ s/(.{60})/$1\n/g;

print "$dna\n";
print OUTFILE "$dna\n";
}

close INPUT;
close INPUT2;
close OUTFILE;
exit;

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this is my attempt, i realise it is bad and can't think of a good way to do this. THANX. lol

Edit kudra, 2002-04-24 Added to title

In reply to in need of wisdom: handling DNA strings by lolly

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