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open INFILE, "$ARGV[0]";

open INFILE, "<", $ARGV[0] or die "Can't read '$ARGV[0]': $!";

# I'd use a better variable than $line, but I don't know
# what your purpose is, and your Tryptic names are quite
...
    $hTryptic{$accSeq} = $line;
    $line = $accSeq;
}

my %in_array_b;
@in_array_b{@array_b} = ();
foreach my $one (@array_a) {
  print $in_array_b{$one} ? $hash_a{$one} : $hash_b{one};
}