in reply to use of uninitialized value in array

...and check that your opens actually work (against possible typo in name, CWD is wrong dir; etc): 

open (HFR, '<', 'HFR_genes.txt') or die "Can't open for reading HFR_ge
+nes.txt, $!";

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Updated to correct file name; miscopied from OP.

My apologies to all those electrons which were inconvenienced by the creation of this post.

In Section Seekers of Perl Wisdom