why do you split this on tabs? If you want to compare the whole line you can compare the lines as in "if ($line_from_hum eq line_from_bact){...}" or something. If you need to extract only a part of the line (say the first three fields) you could use a regex as in:
my ($part_of_line) = ($line=~/^((?:\S+\t){3})/);
One problem in the logic of your code might be that you are comparing lines only from "the point of view" of the human file. Lines in bact that are not in human will not be captured at the moment, which may or may not be what you wanted.
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