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#!/usr/bin/env perl
use strict;
...
s/(.*),$/.$1($1),/ for @r[1..$#r];
$r[-1] =~ s/,$/);/;
print @r;

$ cat input.txt 
module abc(
...
.rist_top_tdi(rist_top_tdi),
.rist_top_tdo(rist_top_tdo));
$