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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++} . . . .

Command Prompt Results:

C:\Documents and Settings\user\Desktop>

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.

In reply to Request to detect the mistake in a perl script for finding inter-substring distance from a large text file by supriyoch_2008

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