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Message: [QUOTE="jamesrwagner, post: 4846552"] Hello: I was basically finding that after a block of code, an array I had called @localizations was still the same size, but each of the variables was now being overwritten by an empty string. What I found on closer inspection was that as I was reading in from the file with handle INPUT, each line was in turn being stored in the current place that it was on from the outer foreach loop, until upon termination when the final line is only a newline storing a n empty string in that place holder. The code below sub indexSequences { my $fold = shift; my $minSup = shift; my @localizations = ("cytoplasmic", "cytoplasmicmembrane", "extracellular", "outermembrane", "periplasmic"); my %containsHash; foreach(@localizations) { my $localization = $_; open INPUT, "freseqs" . $_ . $fold . $minSup ; while(<INPUT>) { chomp; } foreach(@localizations) { my $alocalization = $_; print("This is the $alocalization $_\n"); } } } [/QUOTE]