use strict;
use warnings;
use Data::Dumper;

my @parsed = ();

while (<DATA>) {
    my $in = $_;
    chomp($in);
    my @line = split(/,/, $in);
    for my $i(0..$#line) {
        $parsed[$i] .= $line[$i].'|';
    }
}
map {chop} @parsed;

print Dumper(\@parsed);

__DATA__
123,"text",66,"more text"
124,"text1",67,"more text1"
125,"text2",68,"more text2"

##</code><code>##

$VAR1 = [
          '123|124|125',
          '"text"|"text1"|"text2"',
          '66|67|68',
          '"more text"|"more text1"|"more text2"'
        ];