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Full Discussion: How to extract a subset from a huge dataset
Top Forums Shell Programming and Scripting How to extract a subset from a huge dataset Post 302403613 by cliffyiu on Saturday 13th of March 2010 11:06:43 AM
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!!
 

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LEARN ABOUT CENTOS

hugetlbfs_find_path

HUGETLBFS_FIND_PATH(3)					     Library Functions Manual					    HUGETLBFS_FIND_PATH(3)

NAME

       hugetlbfs_find_path, hugetlbfs_find_path_for_size - Locate an appropriate hugetlbfs mount point

SYNOPSIS

       #include <hugetlbfs.h>

       const char *hugetlbfs_find_path(void);
       const char *hugetlbfs_find_path_for_size(long page_size);

DESCRIPTION

       These  functions  return  a  pathname  for a mounted hugetlbfs filesystem for the appropriate huge page size.  For hugetlbfs_find_path, the
       default huge page size is used (see gethugepagesize(3)).  For hugetlbfs_find_path_for_size, a valid huge page size must be  specified  (see
       gethugepagesizes(3)).

RETURN VALUE

       On success, a non-NULL value is returned.  On failure, NULL is returned.

SEE ALSO

       libhugetlbfs(7), gethugepagesize(3), gethugepagesizes(3)

AUTHORS

       libhugetlbfs was written by various people on the libhugetlbfs-devel mailing list.

								   March 7, 2012					    HUGETLBFS_FIND_PATH(3)
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