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open INFILE, "$ARGV[0]";
@aTryptic = <INFILE>;
...
    $hSemiTryptic{$accSeq} = $aSemiTryptic[$i];
    $aSemiTryptic[$i] = $accSeq;
}

foreach $one (@arrayA) {
    chomp $one;
...
        print "$hashA{$one}";
    }
}