Ok, I'm confused with this one, namely because it used to work for a start! Don't have the faintest idea what has gone wrong now.
I have a text file ... looks similar to this other than it actually has 13 columns 
.55    0.68    0.39    0.69    0.42    0.43    0.52    0.61    
0.13    0.1    0.09    0.06    0.08    0.12    0.07    0.08    
0.04    0.01    0.13    0.04    0.1    0.07    0.03    0.02    
0.08    0.03    0.11    0.03    0.08    0.05    0.07    0.02

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Out of those 13 columns I want to chose any 10 of them and then print them. So, one file might not have columns 1 3 and 6 . Another might not have 4, 7 and 9. I want to create files for all combinations of 10 columns .. making 120 files in total.
I first write a perl program that will give a .txt file like this 
1 10 2
1 10 3
1 10 4
1 10 5
1 10 6
1 10 7
1 10 8
etc

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I then feed this text file into the following perl script 
#! /usr/bin/perl

$combofile = $ARGV[0];

$spectralfile = $ARGV[1];

$diroutput = $ARGV[2];

$without = "spectrawithout";

$txt = ".txt";

open(COMBO, "$combofile") || die "Error: Can't open $combofile: $!\n";

while(<COMBO>)
{

    @combo = split;

    $var1 = $combo[0];
    $var2 = $combo[1];
    $var3 = $combo[2];

    $output = "$without$var1$var2$var3$txt";

    system("chosespectraldata.pl $spectralfile $var1 $var2 $var3 > $di
+routput$output");
}

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Which then calls this one. 
#! /usr/bin/perl

$spectralfile = $ARGV[0];
$var1 = $ARGV[1];
$var2 = $ARGV[2];
$var3 = $ARGV[3];

$count = 0;

open(SPEC, "$spectralfile") || die "ERROR: Can't open $spectralfile FI
+LE for reading: $!\n";

foreach my $line (<SPEC>)
{

    chomp $line;

    #@array = split(/\t/,$line);

    @array = split(/\,/,$line);

    for($i = 0; $i<@array; $i++)
    {

    $count = $i++; 

    if(($count != $var1) || ($count !=$var2) || ($count !=$var3))
    {
        
        print "$count $var1 $var2 $var3\n";

        print "$array[$i],\t";
     
    }
    }
    print "\n";

}

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It doesnt work and I am straching my head as to why. I use the count variable because .. although it used to work for when column = 0, it doesnt now, at all. But the count variable doesnt increase at all, so it doesnt do what I think it should be doing. The files are being created ok but all 13 columns are being printed each time .. so I have 120 files that are exactly the same.
I just know this has to be a silly mistake but I can't find it. Any suggestions much appreciated.

In reply to what on earth is going on? by Angharad

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