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How to extract a subset from a huge dataset

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# 1  
Old 03-13-2010
How to extract a subset from a huge dataset
Hi, All

I have a huge file which has 450G. Its tab-delimited format is as below

Code:
x1 A 50020 1
x1 B 50021 8
x1 C 50022 9
x1 A 50023 10
x2 D 50024 5
x2 C 50025 7
x2 F 50026 8
x2 N 50027 1
:
:

Now, I want to extract a subset from this file. In this subset, column 1 is x10, column 2 is from 600000 to 30000000. I wrote the following perl script but it doesn't work:

Code:
#!/usr/bin/perl

$file1 = $ARGV[0]; # Input file
$file2 = $ARGV[1]; # Output file

open (IN, $file1);
while ($line = <IN>)
{
  chomp($line);
  @array = split(/\t/,$line);

  if ($array[0] eq 'x10')
  {
    if (($array[2] >= 600000) && ($array[2] <= 26279795))
    {
      open (OUT, ">>$file2");
      print OUT "$line\n";
      close OUT;
    }
  }
}
close IN;
exit;

I guess the input file and output file are both too big that my script can't handle it.

Anyone knows if there is any good way to do it? Perl or Shell scripts are preferred..

All your help will be appreciated!
Last edited by Franklin52; 03-13-2010 at 01:47 PM.. Reason: Please indent your code and use code tags!!
# 2  
Old 03-13-2010
Code:
nawk -F"[\t]" '$1~/x10/ && $3>600000  && $3<30000000'  FILE > SubFILE

Last edited by EAGL€; 03-13-2010 at 12:33 PM.. Reason: didnt see it is tab delimeted format.
# 3  
Old 03-13-2010
Hi,Eagle

Thanks for your reply. I just tried your command but it failed. It said

-bash: nawk: command not found

it seems like we don't have nawk in our server.

Do you have other idea? can I just use awk?
# 4  
Old 03-13-2010
Try awk instead or /usr/xpg4/bin/awk on Solaris:

Code:
awk '$1=="x10" && $3>600000 && $3<30000000'  FILE > SubFILE

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