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  1. or download this
    use strict ; use warnings ;

...
data31~data32~data33~data34~"data35"
data,data41~data42~data43~data44~data45
data51,data52,data,junk,specialchar,sometingdata53~data54~data55
  2. or download this
    print join '",', map { s/(\A|"|\n)/"$1/g ; $_ } split /~/ while <DATA>
+;