Creating multiple csv files from data within a csv file

Perl "one-liner"

perl -MText::CSV_XS -e'$c=Text::CSV_XS->new({binary=>1,eol=>"\n"});%a=map{$i++;/^L\d+$/?($_=>$i):()}@{$c->getline(*ARGV)};open$b{$_},">$_"for keys%a;while($f=$c->getline(*ARGV)){$c->print($b{$_},[@$f[0,1,$a{$_}]])for keys%a}'

For ones which have problem with reading:

$ echo '$c=Te...' | perltidy
$c = Text::CSV_XS->new( { binary => 1, eol => "\n" } );
%a = map { $i++; /^L\d+$/ ? ( $_ => $i ) : () } @{ $c->getline(*ARGV) };
open $b{$_}, ">$_" for keys %a;
while ( $f = $c->getline(*ARGV) ) {
    $c->print( $b{$_}, [ @$f[ 0, 1, $a{$_} ] ] )
      for keys %a;
}

Using only AWK:

awk -F, -vOFS=, -vc=1 '
    NR == 1 {
        for (i=1; i<NF; i++) {
            if ($i != "") {
                g[c]=i;
                f[c++]=$i
            }
        }
    }
    NR>2 {
        for (i=1; i < c; i++) {
            print $1,$2, $g[i] > "output_"f[i]".csv"
        }
    }' data.csv

As a one-liner:

awk -F, -vOFS=, -vc=1 'NR == 1 {for (i=1; i<NF; i++) {if ($i != "") {g[c]=i; f[c++]=$i}}} NR>2 { for (i=1; i < c; i++) {print $1,$2, $g[i] > "file_"f[i]".csv" }}' data.csv

Example output:

$ cat file_L1.csv
EXAMPLEfoo,60,6
EXAMPLEbar,30,6
EXAMPLE1,60,3
EXAMPLE2,120,6
EXAMPLE3,60,6
EXAMPLE4,30,6
$ cat file_L2.csv
EXAMPLEfoo,60,0
EXAMPLEbar,30,6
EXAMPLE1,60,3
EXAMPLE2,120,0
EXAMPLE3,60,6
EXAMPLE4,30,6
$ cat file_L11.csv
EXAMPLEfoo,60,0
EXAMPLEbar,30,6
EXAMPLE1,60,3
EXAMPLE2,120,0
EXAMPLE3,60,0
EXAMPLE4,30,6

use strict;
use warnings;

use Text::CSV;
my $csv = Text::CSV->new;

sub parse_line {
    $csv->parse(shift) or die $!;
    return $csv->fields;
}

my @metadata;
my @files  = parse_line(scalar <>);
my @header = parse_line(scalar <>); # Ignore.
for my $i (0 .. $#files){
    next unless length $files[$i];
    open(my $h, '>', "$files[$i].csv") or die $!;
    push @metadata, {column => $i, handle => $h};
}

while (my $line = <>){
    my @fields = parse_line($line);
    for my $m (@metadata){
        $csv->print($m->{handle}, [ @fields[0, 1, $m->{column}] ]);
        print {$m->{handle}} "\n";
    }
}