normalize

#!/usr/bin/perl

use strict;
use Getopt::Std;
use POSIX qw(ceil floor);

my $usage = "Usage: cat file | normalize -c [column] -p [plus] -x [divide] -a > output \n".
    " -a uses the first value found in the first row at column c as the amount to subtract by, i.e. auto normalize";


my %para = ();
getopts('c:p:x:a', \%para);

while (my $line = <STDIN>) {
    next if ($line =~ /^\#/);

    my (@item) = split (/\s/,$line);
    my $i = $item[$para{'c'}];
    my $ip = $i;
    next if (!defined($i));

    if (!defined($para{'p'}) && defined($para{'a'})) {
	$para{'p'} = -1 * $i;
    }

    if (defined($para{'p'})) {
	$i += $para{'p'};
    }

    if (defined($para{'x'})) {
	$i /= $para{'x'};
    }

    #print "was $ip now $i\n";

    $item[$para{'c'}] = $i;

    print "@item\n";




}