So for each line in your file, you want to replace one or more commas at the end of the line, with a single comma - yes?

If that's the case, it's as simple as:

while (<LINES>) {
    $_ =~ s/,+$/,/;
}
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(You could actually do this from the command line with something like: perl -pi -e 's/,+$/,/' file.txt)