Hello, I don't really understand your code :

• You open FILE and you use BLASTX
• You never use the array passed to the sub split_file
• you return an array, that you never use

I would do this :

open FILE, "< $ARGV[0]" or die "Unable to open file : $!\n"
while (<FILE>) {
  push @{$data[$.]}, split /[\s\t]+/;
}
[download]

(No tested)
$. is the line number of the input file. Hence, if you have a test file like this

1 2 3 4
5 6 7 8
9 A B C
[download]

$data[ 2 ] [ 1 ] will give '6'

HTH

-- zejames