#!/usr/bin/perl

use v5.12.2;
use warnings;
use strict;

while (my $line = <DATA>) {
   if ($line =~ /(\d\d)[:;](\d\d)[:;](\d\d)/){  
     my $hours = $1; 
     my $minutes = $2; 
     my $seconds = $3; 
     print "$hours,$minutes,$seconds\n";
   }
   else{
     print qq{bad line: $line\n};
   }
}

__DATA__
01:23:45
06:54;32
23;45:16
23_45_16