If you want to handle this in Perl the best solution is to not use a temp file at all: 
#! /usr/bin/perl
use strict;
use warnings;

my $cmd = "./a.out input.txt";
open(my $pipe, "-|", $cmd) or die "Can't run '$cmd': $!";
my @sequence = <$pipe>;
# Proceed to process output.

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In reply to Re: How to run C object code in PERL by tilly
in thread How to run C object code in PERL by masala_curry

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