I don't know what your input data file looks like (presumably it's plain text containing 5 tab-delimited values per line), but your code could be simplified to the following, in order to do what I think you want:

#!/usr/bin/perl

use warnings;
use strict;

sub read_TABLE
{
    my ( $filename ) = @_;
    open( TBL, $filename ) or die "cannot open $filename: $!\n";

    my @table;
    while ( <TBL> ) {
        chomp;
        push @table, [ split( /\t/, $_ , 5 ) ];
    }
    close TBL;
    return @table;
}

for my $row ( read_table( "TABLE.txt" )) {
    my ( $start, $end, $name, $strand, $type ) = @$row;
    print "$type\n";
}
[download]

Some notes:

• As mentioned in the first reply, you should only call "open()" once before reading a given file, and test the return from that one call.

• You don't need the "temporary" arrays to store lists of things; when a sub or function call returns a list, you can use the call directly as input a "for" loop, or as the content of an anonymous array creation (e.g. putting "split()" between square brackets).

• The "read_table" function is returning a list of array references, so in the main part of the code, the "for" loop treats each value returned by "read_table" as an array reference (@$row).

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