Perl code Out of memory problem

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# 1  
Old 09-11-2011
Perl code Out of memory problem

Hi I am working with a 3.0 GB file and running the following script to process it. After running for 15 minutes, the script stops saying Out of memory or Killed.

Can the experts suggest where my code can be improved to save memory?

Thanks in advance.

#! usr/bin/perl
use warnings;
open RAW, "$ARGV[1]";
open ADAPTER, "$ARGV[0]";
@reads =();
@ada =();
while (<RAW>) {
      if (($. -2) % 4 == 0) {push (@reads, $_);             
while (<ADAPTER>) {                                                    @adapter = split (//);
            $i= -1;
        while (++$i < $#adapter-8) {
                            $_ = "$adapter[$i]$adapter[$i+1]$adapter[$i+2]$adapter[$i+3]$adapter[$i+4]$adapter[$i+5]$adapter[$i+6]$adapter[$i+7]$adapter[$i+8]";
                             push (@ada, $_);                             
@reads1 = ();
foreach $reads(@reads) {                              
             foreach $ada(@ada) {
                                  $reads =~ s/$ada.*|(A{9}|G{9}|C{9}|T{9})[A-Z]+//g; 
                       push (@reads1, $reads);  
%duplicates = ();
chomp (@reads1);
$i = 0;
open Fasta_reads, ">/home/Desktop/fasta_reads";
foreach (@reads1) { 
            if (length $_ >14) {                                      
                  }            }
foreach $count (keys %duplicates) {$i +=1;
               $read_length = length $count;
               $_ = "> $i $read_length $duplicates{$count}\n$count\n";
               print Fasta_reads;
                                  } close Fasta_reads;

# 2  
Old 09-11-2011
It's hard and unpleasant to read code without the description of your problem, comments and sample input/output. I'm going to admire a man who can help you.
# 3  
Old 09-11-2011
Originally Posted by yazu
It's hard and unpleasant to read code without the description of your problem, comments and sample input/output. I'm going to admire a man who can help you.
sorry - I didnt think the purpose of code is relevant here. But these are the steps I am following in the code.

I have a 3 GB text file with DNA sequence reads.
1. I extract reads at specific line numbers
2. substitute reads containing some expressions. These expressions are chopped from a single DNA adapter sequence.
3. count the duplicates
4. extract reads of only >14 length.
5. add > sign and serial number and length to each read to make it suitable for downstream purposes.

It appears that the problem is stemming from too much usage of arrays. If I split the code and use filehandles, it is able to execute the code but still its taking a very long time.

I started to think that AWK is much faster than Perl.Smilie

# 4  
Old 09-11-2011
What do those two files you pass as parameters look like?

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