Re: extracting columns

[Marshall]

When you do something other than the default split, you need to specify the variable to split upon.

my @fields = split /\t/;
should be:
my @fields = split /\t/,$_;

Add tags around code so that it appears formatted correctly in the post. <code>...your code here</code>
Oh, I see <\code> should be </code>

before the print, just skip the print and loop for next line if $SIZE doesn't meet the criteria:

 
next unless ($SIZE >2.0 and $SIZE < 5.0);

[perllearner007]

Hi Marshall, Thanks for the reply. However, changing to my @fields = split /\t/,$_;hasn't resolved the issue. I still get the same output. Thanks for pointing out the <\code> error!

[Marshall]

Thanks for the code tag change! Now I can read it.
Evidently, you do not need the 2nd arg in the split(), my memory was faulty, Ooops.

When you add in the $SIZE comparison, you need to do something about the line that is not numeric (the first header line) - otherwise the comparison will fail with "$SIZE not numeric". You could read and deal with that first line before the loop or below I added a test in the "if" to check that it is numeric before doing the comparison. In the "if" if $SIZE doesn't start with 0-9 or the "minus sign" or period, then rest of the "if" is skipped and the line is printed.

I usually add a "skip blank" line statement in these things as sometimes there is a trailing blank line that causes trouble- that's purely optional.

#!usr/bin/perl -w
use strict;

while(<DATA>)
{
    next if /^\s$/;        # skip blank lines
    
    my ($SAMPLE_NAME, $SIZE) = (split /\s+/)[1,3]; 
    
    # print line if $SIZE isn't numeric, e.g. "SIZE"
    # or if it is a number, then must meet min, max criteria
    
    if ($SIZE =~ /^[^0-9-.]/ or ( $SIZE > 2 and $SIZE <5)) 
    {
       print "$SAMPLE_NAME $SIZE\n";
    }
}

=prints
SAMPLE_NAME SIZE
U7345 4.333
=cut 
        
__DATA__
ID SAMPLE_NAME EFFECTS SIZE
001 U7654 NEGATIVE 5.666
002 U7345 POSITIVE 4.333
003 U7674 NEGATIVE 1.696
002 U7845 POSITIVE -4.333

[perllearner007]

Thanks Marshall. I do get the extracted columns but it gives me all the values even after I set the size limitation.

[perllearner007]

Thank you! There was an error in the data! It is resolved now!