Hello, wise ones! I am trying to read in a file with content like this: 

TATTATGAGAATAGTGTGCATTTT    3
ATAGAGCAAAAGGGCAAATGCTGA    6
TACGAGTAGGATATCGATCTGGTGG    2
ATCCCCGGCATCTCCGCCA    1
TGAGAATAGTGTGCATTT    52
CGCATTACATTTGGAGCC    1
ACTCCAGGCAGCGTAGAGTT    1
ATCAACGTTGCTGCATCGG    1

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It is a tab demilimited file. I want to manipulate the file to have it look like this: 
>dme0_count=3
TATTATGAGAATAGTGTGCATTTT    
>dme1_count=6
ATAGAGCAAAAGGGCAAATGCTGA    
>dme2_count=52
TGAGAATAGTGTGCATTT

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(i). Sequences(column 0) with length less than 15 or greater than 30 are ommitted (ii). Sequences with counts (Column 1) < 2 are ommitted (iii). the print statement takes uses an argument and the count for the header line. Here is my code: 

#!/usr/bin/perl -w

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>)
{
foreach my $line ($tabdata){
    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);

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Here is the error:
a> line 1.
Use of uninitialized value $fields[1] in numeric gt (>) at tab.pl line
+ 19, <$tabdata> line 2.
Use of uninitialized value $fields[1] in numeric gt (>) at tab.pl line
+ 19, <$tabdata> line 3.
.
.
.
Use of uninitialized value $fields[1] in numeric gt (>) at tab.pl line
+ 19, <$tabdata> line 21.

[download]

I'd appreciate some assistance on how to get this to work! Thank you.

In reply to Manipulating tab delimited file by andyBio

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