I can't see why backticks won't work: 
  my @output_lines_array = `/path/to/your_executable`;
  foreach my $line (@output_lines_array) {
     if (/^No. of sequences \(letters\): ([\d,])\s/) {
        print "No. of sequences = $1\n";
     }
  }

[download]
I'm a little out of practice so beware, but hopefully it's close.

In reply to Re: capture STDOUT without printing to screen by hmerrill
in thread capture STDOUT without printing to screen by k99ja04

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