It's not at all clear what the bigger picture is, but if you want to subsequently do some sort of lookup to find the genes associated with a particular operon the generating a hash is more useful. Consider:

use strict;
use warnings;

my %operons;

while (<DATA>) {
    chomp;
    next unless /^(\S+) \s+\S+\s+\S+\s+ (\S+)$/x;
    
    my ($operon, $targets) = ($1, $2);
    my @genes = split /,/, $targets;
    
    $operons{$operon} ||= {};
    
    for (@genes) {
        my ($subOperon, $gene) = /([^|]*)\|(.*)/;
        
        $operons{$operon}{$subOperon} = $gene;
    }
}

for my $operon (sort keys %operons) {
    print "$operon: ",
        join (', ', map {"$_ ($operons{$operon}{$_})"} sort keys %{$op
+erons{$operon}}),
        "\n";
}

__DATA__
malS    1    forward    malS|b3571,
malT    1    forward    malT|b3418,
malXY    2    forward    malX|b1621,malY|b1622,
malZ    1    forward    malZ|b0403,
manA    1    forward    manA|b1613,
manXYZ    3    forward    manX|b1817,manY|b1818,manZ|b1819,
map-glnD-dapD    3    reverse    dapD|b0166,glnD|b0167,map|b0168,
marC    1    reverse    marC|b1529,
marRAB    3    forward    marA|b1531,marB|b1532,marR|b1530,
mbhA    1    forward    mbhA|,
mcrA    1    forward    mcrA|b1159,
mcrBC    2    reverse    mcrB|b4346,mcrC|b4345,
mdaB    1    forward    mdaB|b3028,
mdh    1    reverse    mdh|b3236,
mdlAB    2    forward    mdlA|b0448,mdlB|b0449,
mdoB    1    reverse    mdoB|b4359,
mdoC    1    reverse    mdoC|b1047,
mdoD    1    forward    mdoD|b1424,
mdoGH    2    forward    mdoG|b1048,mdoH|b1049,
mdtABCD-baeSR    6    forward    baeR|b2079,baeS|b2078,mdtA|b2074,mdtB
+|b2075,mdtC|b2076,mdtD|b2077,
mdtEF    2    forward    mdtE|b3513,mdtF|b3514,
mdtG    1    reverse    mdtG|b1053,
mdtH    1    reverse    mdtH|b1065,
mdtJI    2    reverse    mdtI|b1599,mdtJ|b1600,
mdtK    1    forward    mdtK|b1663,
mdtL    1    forward    mdtL|b3710,
mdtM-yjiN    2    reverse    mdtM|b4337,yjiN|b4336,
mdtNOP    3    reverse    mdtN|b4082,mdtO|b4081,mdtP|b4080,
mdtQ    1    reverse    mdtQ|b2138,
melAB    2    forward    melA|b4119,melB|b4120,
melR    1    reverse    melR|b4118,
menA    1    reverse    menA|b3930,
menFD-yfbB-menBCE    6    reverse    menB|b2262,menC|b2261,menD|b2264,
+menE|b2260,menF|b2265,yfbB|b2263,
metA    1    forward    metA|b4013,
metBL    2    forward    metB|b3939,metL|b3940,
metC    1    forward    metC|b3008,
metE    1    forward    metE|b3829,
metF    1    forward    metF|b3941,
metG    1    forward    metG|b2114,
metH    1    forward    metH|b4019,
metJ    1    reverse    metJ|b3938,
metK    1    forward    metK|b2942,
metNIQ    3    reverse    metI|b0198,metN|b0199,metQ|b0197,
metR    1    reverse    metR|b3828,
metT-leuW-glnUW-metU-glnVX    7    reverse    glnU|b0670,glnV|b0665,gl
+nW|b0668,glnX|b0664,leuW|b0672,metT|b0673,metU|b0666,
metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp    8    reverse    infB|b3168,m
+etY|b3171,nusA|b3169,pnp|b3164,rbfA|b3167,rpsO|b3165,truB|b3166,yhbC­
+|b3170,
metZWV    3    forward    metV|b2816,metW|b2815,metZ|b2814,
mfd    1    reverse    mfd|b1114,
mglBAC    3    reverse    mglA|b2149,mglB|b2150,mglC|b2148,
mgrB    1    reverse    mgrB|b1826,
mgsA    1    reverse    mgsA|b0963,
mgtA    1    forward    mgtA|b4242,
[download]

Prints:

malS: malS (b3571)
malT: malT (b3418)
malXY: malX (b1621), malY (b1622)
malZ: malZ (b0403)
manA: manA (b1613)
manXYZ: manX (b1817), manY (b1818), manZ (b1819)
map-glnD-dapD: dapD (b0166), glnD (b0167), map (b0168)
marC: marC (b1529)
marRAB: marA (b1531), marB (b1532), marR (b1530)
mbhA: mbhA ()
mcrA: mcrA (b1159)
mcrBC: mcrB (b4346), mcrC (b4345)
mdaB: mdaB (b3028)
mdh: mdh (b3236)
mdlAB: mdlA (b0448), mdlB (b0449)
mdoB: mdoB (b4359)
mdoC: mdoC (b1047)
mdoD: mdoD (b1424)
mdoGH: mdoG (b1048), mdoH (b1049)
mdtABCD-baeSR: baeR (b2079), baeS (b2078), mdtA (b2074), mdtB (b2075),
+ mdtC (b2076), mdtD (b2077)
mdtEF: mdtE (b3513), mdtF (b3514)
mdtG: mdtG (b1053)
mdtH: mdtH (b1065)
mdtJI: mdtI (b1599), mdtJ (b1600)
mdtK: mdtK (b1663)
mdtL: mdtL (b3710)
mdtM-yjiN: mdtM (b4337), yjiN (b4336)
mdtNOP: mdtN (b4082), mdtO (b4081), mdtP (b4080)
mdtQ: mdtQ (b2138)
melAB: melA (b4119), melB (b4120)
melR: melR (b4118)
menA: menA (b3930)
menFD-yfbB-menBCE: menB (b2262), menC (b2261), menD (b2264), menE (b22
+60), menF (b2265), yfbB (b2263)
metA: metA (b4013)
metBL: metB (b3939), metL (b3940)
metC: metC (b3008)
metE: metE (b3829)
metF: metF (b3941)
metG: metG (b2114)
metH: metH (b4019)
metJ: metJ (b3938)
metK: metK (b2942)
metNIQ: metI (b0198), metN (b0199), metQ (b0197)
metR: metR (b3828)
metT-leuW-glnUW-metU-glnVX: glnU (b0670), glnV (b0665), glnW (b0668), 
+glnX (b0664), leuW (b0672), metT (b0673), metU (b0666)
metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp: infB (b3168), metY (b3171), nu
+sA (b3169), pnp (b3164), rbfA (b3167), rpsO (b3165), truB (b3166), yh
+bC­ (b3170)
metZWV: metV (b2816), metW (b2815), metZ (b2814)
mfd: mfd (b1114)
mglBAC: mglA (b2149), mglB (b2150), mglC (b2148)
mgrB: mgrB (b1826)
mgsA: mgsA (b0963)
mgtA: mgtA (b4242)
[download]