Well for a start you're not setting $line to anything.

Try something along these lines :-

while (my $line = <MOTIFS>) {
    chomp $line;
    ...
}

[download]

It's worth reading the Basic Debugging Checklist - or how to find out what's going on when your code doesn't work.

In reply to Re: reading in different sizes of matrix by RichardK
in thread reading in different sizes of matrix by LostWeekender

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