use strict;
use warnings ;


my @csv = <DATA>;

foreach my $line ( @csv ) { 
    my $clean_line = $line ;
    while( $line =~ /"(.*?)"/g ) { 
	my $match = $1 ;
	my $match_cleaned = $match ;
	$match_cleaned =~ s/,/~/g;
	my $location = index( $line, $match ) ;
	my $clean_line = substr( $clean_line, $location, length( $match ), $match_cleaned );
    }
    print "$clean_line";
}

__DATA__
123,abc1,test1,"1,3,5",new,"abc,dfg,hj"
124,abc2,test2,"1,3,5",new,"abc,dfg,hj"
125,abc3*,test3,"*|1,3,5",new,"abc,dfg,hj"