perlquestion
supriyoch_2008
<p>Hi Perl Monks,</p>
<P>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.</p> <p>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. </p><p>Furthermore, I need the syntax at the initial part to assign the input large file to an array variable like<code> my @lines </code>so that I can assign this array to a scalar variable like<code> my $string ="@lines"; </code>for use in later part of the script.</p>
<code>#!/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++}
. . . . </code>
<p>Command Prompt Results:</p>
<p>C:\Documents and Settings\user\Desktop>m3.pl</p>
<p>Please type the filename of the DNA sequence data: chr1.txt</p>
<p>Number of bases: 219475005.</p>
<p>A=63473407; T=63582431; G=45425056; C=45435903; Errors(N)=1558208.</p>
<p>Enter a motif to count nt between two such motifs: GAATTCCT</p>
<p>I found the motif!</p>
<p>Out of memory!</p>
<p>C:\Documents and Settings\user\Desktop></p>
<p>Thanks to Perl Monks for their quick reply in solving perl problems.</p>