I definitely agree with the three-argument syntax you are suggesting, but I think that MidLifeXis's comment was even more important: checking whether the file could be open. I would therefore suggest this possible syntax:

my $input_file = "/Users/Desktop/Pipelines/fungi.1.aa.hypothetical.faa
+");
my $output_file = "Users/Desktop/Pipelines/fungi.1.aa.hypothetical50.f
+aa");
open my $in, '<', $input_file or die "could not open $input_file $!";
open my $out, '>', $output_file or die "could not open $output_file $!
+";
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