It's not too clear what ###How should I do this? means, but my reading of it suggests that you might be trying to compile & run the C code (c/w writing a perl script to emulate your C code) something along the following lines ...

use warnings;
use strict;

system 'gcc cProg.c';
die "Compile failed - $!" if $? >> 8;
system './a.out input.txt > output.txt';
die "Run failed"  if $? >> 8;
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I used system, since there is no (apparent) requirement to capture output - only to run the command and continue dependant on the success status.

Your comment tosses the contents of "output.txt" in an array "@sequence" to work on is only true in the context of a file containing a single line - as in your example.

If it were a multi-line file, you might want to undef the input record separator ($/ - see perlvar) in order to slurp the file into the array in one operation.