use strict;
my $str = '#,0001,0110,0010:~;0101_1000;0110_1001;0111_1010;1000_1011;1001_1100;1010_1101;1011_1110;1100_1111,~0_00001_00012_00103_00114_01005_01016_01107_01118_10009_1001,';
my $regex = qr/(\d)(,)(\d{3})(?=(?=.*?:).*?~.*?;0*\1\3_(.)(.{3}))|(\d)(,)(\d{3})(?=.*?:)|(\d)(:)|(#),/p;
my $subst = '$2$7$4$6$5$8$10$9$11';
my $result = $str =~ s/$regex/$subst/rg;
print "The result of the substitution is' $result\n";
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for Perl, please visit: http://perldoc.perl.org/perlre.html