Here is the simple regex logic without spliting the input 
#! /usr/bin/perl

use strict;
use warnings;

open my $fh,">","tmp.csv" or die "Unable to open $! \n";
while(<DATA>){
        $_ =~ s/(\S+,)+([^~]*)/"$1$2"/g if $_ =~ /,/;
        $_ =~ s/~/,/g;
        print $fh "$_";
}
close $fh;

__DATA__
col1~col2~col3~col4~col5
data11~data12~data13~data14~data15
data21~data22~data23~data24~data25
data31~data32~data33~data34~data35
data,data41~data42~data43~data44~data45
data51,data52,data,junk,specialchar,sometingdata53~data54~data55

[download]

In reply to Re: Workaround for my CSV file by brsaravan
in thread Workaround for my CSV file by harishnuti

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.