tempProteinFamFileCreator();
...
sub tempProteinFamFileCreator 
{
my $infile = $ARGV[0]."_ProFam";
##</code><code>##

...
tempProteinFamFileCreator( @ARGV );
...
sub tempProteinFamFileCreator {
    my  $infile   = $_[0] .'_ProFam';
# or
#   my  $infile   = shift .'_ProFam';


...

##</code><code>##

 @ARGV = ( 1 , 2 , 3 );
print @ARGV;

##</code><code>##

print 1,2,3;