Hi Perl Monks,

I am a beginner in perl programming. I have written a perl script which can read a small text file and gives correct results for inter-substring distance in cmd in Windows XP. But cmd shows the problem of “out of memory” when I try to analyze a large text file with 219475005 letters for finding the inter-substring distance although the program counts the number of each letter in the file correctly within 2 minutes but fails to find the inter-substring distance. I think this could due to incorrect reading of file.

So I have given the initial part of the script and the results of cmd screen below. I am seeking your suggestions to rectify the mistake in the script for analyzing a large file.

Furthermore, I need the syntax at the initial part to assign the input large file to an array variable like my @linesso that I can assign this array to a scalar variable like my $string ="@lines";for use in later part of the script.

#!/usr/bin/perl –w
print "\n\nPlease type the filename: ";
$DNAfilename = <STDIN>;
chomp $DNAfilename;
# open the large file
unless ( open(DNAFILE, $DNAfilename) ) {
print "Cannot open file \"$DNAfilename\"\n\n";
exit;
} 
my @lines = <DNAFILE>; 
while (<DNAFILE>) {
  say $_;
} 
close DNAFILE;
$DNA = join( '', @lines);
# Remove whitespace
$DNA=~ s/\s//g;
# Count number of bases
$b=length($DNA);
print "\nNumber of bases: $b.";
# Count number of each base and nonbase
$A=0;$T=0;$G=0;$C=0;$e=0; 
while($DNA=~ /A/ig){$A++}
while($DNA=~ /T/ig){$T++}
while($DNA=~ /G/ig){$G++}
while($DNA=~ /C/ig){$C++}
while($DNA=~ /[^ATGC]/ig){$e++}
. . . .
[download]

Command Prompt Results:

C:\Documents and Settings\user\Desktop>m3.pl

Please type the filename of the DNA sequence data: chr1.txt

Number of bases: 219475005.

A=63473407; T=63582431; G=45425056; C=45435903; Errors(N)=1558208.

Enter a motif to count nt between two such motifs: GAATTCCT

I found the motif!

Out of memory!

C:\Documents and Settings\user\Desktop>

Thanks to Perl Monks for their quick reply in solving perl problems.