How to extract a subset from a huge dataset Post: 302403613

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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

03-13-2010

Registered User

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!!

cliffyiu

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LEARN ABOUT DEBIAN

svm-subset

svm-subset(1)							   User Manuals 						     svm-subset(1)

NAME

       svm-subset - a subset selection tool for LIBSVM

SYNOPSIS

       svm-subset [ -s method ] dataset number [ output1 ] [ output2 ]

DESCRIPTION

       Training  large data is time consuming. Sometimes one should work on a smaller subset first. The python script subset.py randomly selects a
       specified number of samples. For classification data, we provide a stratified selection to ensure the same class distribution in  the  sub-
       set.

OPTIONS

       -s method

       0      -- stratified selection (classification only) (default)

       1      -- random selection

       output1
	      The subset. If output1 is omitted, the subset will be printed on the screen.

       output2
	      The rest of data.

FILES

       See svm-train(1) for the format of dataset

EXAMPLES

	      svm-subset heart_scale 100 file1 file2

       From heart_scale 100 samples are randomly selected and stored in file1. All remaining instances are stored in file2.

BUGS

       Please report bugs to the Debian BTS.

AUTHOR

       Chih-Chung Chang, Chih-Jen Lin <cjlin@csie.ntu.edu.tw>, Chen-Tse Tsai <ctse.tsai@gmail.com> (packaging)

SEE ALSO

       svm-train(1), svm-predict(1)

Linux								     DEC 2009							     svm-subset(1)

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