Hi Perl Monks,

I am a beginner in perl programming. I have written a PERL program to count the number of bases in a DNA molecule from a text file in command prompt in Windows XP. The program works well with small text files having DNA sequence data and gives correct results.

But when I tried to count the number of bases from a 299 MB text file, the program shows “out of memory” in cmd after nearly 2 minutes. One Perl monk suggested me to use Tie: : File to solve this problem. I looked for the syntax of Tie : : File in internet but could not make out how to use it in my program with  <STDIN> input operator assigned to a scalar variable like $DNAfilename=<STDIN>;

I have given the perl program below. May I expect to get help from any perl monk to sort out this problem in my program either using Tie : : File or other method so that I can analyze a 299MB text file. I have a 2-GB RAM in my laptop with Active Perl 5.10.1 Build 1007 version.

Can I use a code like  %mem=300 MW; in perl because this type of code is used by some theoretical and physical chemists in specific programs based on c programming for “Quantitative Structure Analysis and Report (QSAR)” for biomolecules to solve memory problem? 

#!usr/bin/perl 
print "\n\nPlease type the filename of the DNA sequence data: ";
$DNAfilename=<STDIN>;
chomp $DNAfilename;
unless ( open(DNAFILE, $DNAfilename) ) {
    print "Cannot open file \"$DNAfilename\"\n\n";
exit;
}
while(@DNA= <DNAFILE>) {
    $DNA=join('',@DNA);
close DNAFILE;
# Remove whitespace
$DNA=~ s/\s//g;
# Remove whitespace
$DNA=~ s/\s//g;# Line 15
# Count number of bases
$b=length($DNA);
print "\nNumber of bases: $b.\nDoes the value tally with GenBank recor
+d? If yes,continue.";
# Count number of each base and nonbase
$A=0;$T=0;$G=0;$C=0;$e=0; # Line 20
while($DNA=~ /A/ig){$A++}
while($DNA=~ /T/ig){$T++}
while($DNA=~ /G/ig){$G++}
while($DNA=~ /C/ig){$C++}
while($DNA=~ /[^ATGC]/ig){$e++} 
# Line 25
print "\nA=$A; T=$T; G=$G; C=$C; Errors(N)=$e.\n.";
}
exit;

[download]

I have given the cmd output below.

Microsoft Windows XP Version 5.1.2600

(C) Copyright 1985-2001 Microsoft Corp.

C:\Documents and Settings\user>cd d*

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

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

Out of memory!

C:\Documents and Settings\user\Desktop>

I am ever grateful to perl monks for their quick reply with suggestions.

In reply to Seeking help for using Tie : : File in my perl program for counting bases using Active Perl 5.10.1 Build 1007 by supriyoch_2008

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