Thanks for help and input. below code works fine:

my $file = "t.txt";
open(FH,$file) || die "can't open file \n";
while (<FH>) {
    chomp;
    my $line = $_;
    $line =~ s/\"(.*?)\"/replace($1)/ge;
    $line =~ s/\,/~/g;
    $line =~ s/\;/,/g;
    print "$line \n";
}
close FH;
sub replace {
    my ($str) = @_;
    $str =~ s/\,/\;/g;
    return $str;
}
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