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Message: [QUOTE="jamesrwagner, post: 4846553"] 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"); } } } Giving the following output: This is the localization This is the localization cytoplasmicmembrane This is the localization extracellular This is the localization outermembrane This is the localization periplasmic This is the localization This is the localization This is the localization extracellular This is the localization outermembrane This is the localization periplasmic This is the localization This is the localization This is the localization This is the localization outermembrane This is the localization periplasmic This is the localization This is the localization This is the localization This is the localization This is the localization periplasmic This is the localization This is the localization This is the localization This is the localization This is the localization Thus in turn the each element of the @localizations array is overwritten with an empty string. When I comment out the file I/O lines the problem goes away. (And the chomp makes no difference). What can be going on the reading in from a file is overwriting elements of an array? Thanks very much. [/QUOTE]

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