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#!/usr/bin/perl

...
open my $handle, '<', $filename or die "$! opening $filename";
my @array = map s/>\z//r =~ s/^(?!>)/>/r, do { local $/ ="\n>"; <$hand
+le> };
use Data::Dumper; print Dumper \@array;

#!/usr/bin/perl

...
open my $handle, '<', $filename or die "$! opening $filename";
my @array = split /(?=>)/, do { local $/; <$handle> };
use Data::Dumper; print Dumper \@array;