When line 48 of your script is this: 
print "$sequence\n";

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And the warning that perl gives you is "use of uninitialized value $sequence in … string", it means that as of line 48 in your script, no value has ever been assigned to the variable $sequence.

If that fact does not agree with your assumptions about the state of things when your script reaches line 48, then your assumptions are wrong, and this is probably related to the fact that when you try to use $sequence as a hash key, you don't get what you expect.

You could try forming a minimal, self-contained, runnable (small) script that demonstrates the problem you're having, and if that exercise by itself doesn't reveal the problem for you, post that script in full.

In reply to Re^3: hash access with a variable by graff
in thread hash access with a variable by LostWeekender

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