The while loop will iterate through all the lines of your input file, so the foreach loop is unecessary. Also, a chomp is needed in order to avoid extraneous newlines in your output. This edited version of your code seems to work.

#!/usr/bin/env perl

use strict;
use warnings;

my $species=$ARGV[0];
my $input=$ARGV[1];
my @fields;
my $n = 0;

open my $tabdata, '<', "$input" or die ("Can't open $input\n"); 

while  (my $line = <$tabdata>) {
    chomp $line;
    my @fields = split("\t",$line);
    if(($fields[1] > 2) && (length($fields[0]) > 14 && length($fields[
+0]) < 31)) {
            print ">$species" . $n++ . "_count=$fields[1]\n$fields[0]\
+n";
    }
}
close ($tabdata);

exit;

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In reply to Re: Manipulating tab delimited file by kevbot
in thread Manipulating tab delimited file by andyBio

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