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#include< stdio.h>
main (int argc, char *argv[])
...
        }
        return 0;
}

#!/usr/bin/perl
...
$output_file="output.txt";
open(OP, $output_file) || die("Could not open file!");
@sequence=<OP>;     # tosses the contents of "output.txt" in an array 
+"@sequence" to work on.