func2(func1(input1, input2), input3)

##</code><code>##

func1(input1, func2(input2, input3))

##</code><code>##

while (<>) {
    $line = $_;
    $line =~ s/func1\((.*?)\)/proc1{$1}/g;
    $line =~ s/func2\((.*?)\)/FUNC $1 END/g;
    $line =~ s/{/(/g;
    $line =~ s/}/)/g;
    print $line;
}

##</code><code>##

proc1(input1, FUNC input2, input3) END
FUNC input1, proc1(input2, input3) END

##</code><code>##

proc1(input1, FUNC input2, input3 END)
FUNC input1, proc1(input2, input3) END