open INFILE, "$ARGV[0]";

##</code><code>##

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

##</code><code>##

# I'd use a better variable than $line, but I don't know
# what your purpose is, and your Tryptic names are quite
# cryptic for me.
for my $line (@aTryptic) {
    my $accSeq = SplitFields($line], 'split');
    $line =~ s/\r?\n\z//g;
    $hTryptic{$accSeq} = $line;
    $line = $accSeq;
}

##</code><code>##

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};
}