I chose not to assume that an operon was unique thoughout the file, since it wasn't explicitly stated in the spec.

If I can assume uniqueness, then I'd remove the push and change to a HoA:

$hash->{$fields[0]} = \@genes;
[download]

Thanks, I was trying this but failing.

#!/usr/bin/perl


use strict;

my $operon; 
my %operonHash; 


while (<>) { 

chomp; 
if ( /(\b.+?\b)/ ) { # word boundary + any character at least once, up
+ to the first word boundary. 
    #print "Matched: |$`<$&?>$'|\n"; 
    $operon = $_; 
    #print  $& . " " ; 
    $operonHash{$&} = ();  
    } else { 
    print "No match. \n";
    }
    
    print "\n"; 
    
if ( /\w+\|/ ) { # word boundary + any character at least once, up to 
+the first word boundary. 
    print "Matched: |$`<<$&>>$'|\n"; 

    } else { 
    print "No match. \n";
    }

}
[download]

#The problem is, 1. How to get rid of the | from the expression that was found, and 2. How to get MULTIPLE genes before | when more than one gene appears on a line?

From inspection, I noticed that there always seemed to be four spaces delimiting the columns. In the data set provided here, it does not seem the case (ie. there are tabs instead).

If tabs are the actual delimiter, then use this line instead:

my @fields = split(/\t/, $_);
[download]

The initial goal is to split each line of data into four separate fields.


Where do you want *them* to go today?

 

C0067    1    forward    C0067|,
C0293    1    forward    C0293|,
C0343-dbpA    2    forward    C0343|,dbpA|b1343,
C0465    1    forward    C0465|,
C0614    1    reverse    C0614|,
C0719    1    forward    C0719|,
IS128    1    forward    IS128|,
aaeR    1    forward    aaeR|b3243,
aaeXAB    3    reverse    aaeA|b3241,aaeB|b3240,aaeX|b3242,
aas-ygeD    2    reverse    aas|b2836,ygeD|b2835,
aat    1    reverse    aat|b0885,
abgABT-ogt    4    reverse    abgA|b1338,abgB|b1337,abgT|b1336,ogt|b13
+35,
abgR    1    forward    abgR|b1339,
abrB    1    reverse    abrB|b0715,
accA    1    forward    accA|b0185,
accBC    2    forward    accB|b3255,accC|b3256,
accD    1    reverse    accD|b2316,
aceBAK    3    forward    aceA|b4015,aceB|b4014,aceK|b4016,
ackA-pta    2    forward    ackA|b2296,pta|b2297,
acnA    1    forward    acnA|b1276,
acnB    1    forward    acnB|b0118,
acpH    1    reverse    acpH|b0404,
acpT    1    forward    acpT|b3475,
acrAB    2    reverse    acrA|b0463,acrB|b0462,
acrD    1    forward    acrD|b2470,
acrEF    2    forward    acrE|b3265,acrF|b3266,
acrR    1    forward    acrR|b0464,
acs-yjcH-actP    3    reverse    acs|b4069,actP|b4067,yjcH|b4068,
ada-alkB    2    reverse    ada|b2213,alkB|b2212,
add    1    forward    add|b1623,
ade    1    forward    ade|b3665,
adhE    1    reverse    adhE|b1241,
adhP    1    reverse    adhP|b1478,
adiA    1    reverse    adiA|b4117,
adiC    1    reverse    adiC|b4115,
adiY    1    reverse    adiY|b4116,
adk    1    forward    adk|b0474,
adrA    1    forward    adrA|b0385,
aegA    1    reverse    aegA|b2468,
aer    1    reverse    aer|b3072,
aes    1    reverse    aes|b0476,
agaR    1    reverse    agaR|b3131,
agaS-kbaY-agaBCDI    6    forward    agaB|b3138,agaC|b3139,agaD|b3140,
+agaI|b3141,agaS|b3136,kbaY|b3137,
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,


which gives output 


$VAR1 = {
          'malZ' => [
                      [
                        'b0403'
                      ]
                    ],
' => [    'ada-alkB     2       reverse ada|b2213,alkB|b2212,
                                                           []
                                                         ],
          'malS' => [
                      [
                        'b3571'
                      ]
                    ],
' => [    'acnA 1       forward acnA|b1276,
                                             []
                                           ],
' => [    'aegA 1       reverse aegA|b2468,
                                             []
                                           ],
' => [    'adhP 1       reverse adhP|b1478,
                                             []
                                           ],
' => [    'abgABT-ogt   4       reverse abgA|b1338,abgB|b1337,abgT|b13
+36,ogt|b1335,
                                                                      
+             []
                                                                      
+           ],
' => [    'acnB 1       forward acnB|b0118,
                                             []
                                           ],
' => [    'acpT 1       forward acpT|b3475,
                                             []
                                           ],
' => [    'ade  1       forward ade|b3665,
                                           []
                                         ],
' => [    'acrD 1       forward acrD|b2470,
                                             []
                                           ],
' => [    'acpH 1       reverse acpH|b0404,
                                             []
                                           ],
' => [    'agaR 1       reverse agaR|b3131,
                                             []
                                           ],
' => [    'C0293        1       forward C0293|,
                                          []
                                        ],
          'malXY' => [
                       [
                         'b1621',
                         'b1622'
                       ]
                     ],
' => [    'aaeR 1       forward aaeR|b3243,
                                             []
                                           ],
' => [    'ackA-pta     2       forward ackA|b2296,pta|b2297,
                                                           []
                                                         ],
' => [    'aceBAK       3       forward aceA|b4015,aceB|b4014,aceK|b40
+16,
                                                                     [
+]
                                                                   ],
' => [    'aat  1       reverse aat|b0885,
                                           []
                                         ],
' => [    'acrR 1       forward acrR|b0464,
                                             []
                                           ],
' => [    'accA 1       forward accA|b0185,
                                             []
                                           ],
' => [    'IS128        1       forward IS128|,
                                          []
                                        ],
' => [    'aaeXAB       3       reverse aaeA|b3241,aaeB|b3240,aaeX|b32
+42,
                                                                     [
+]
                                                                   ],
          'malT' => [
                      [
                        'b3418'
                      ]
                    ],
' => [    'abrB 1       reverse abrB|b0715,
                                             []
                                           ],
' => [    'C0465        1       forward C0465|,
                                          []
                                        ],
' => [    'aas-ygeD     2       reverse aas|b2836,ygeD|b2835,
                                                           []
                                                         ],
' => [    'C0614        1       reverse C0614|,
                                          []
                                        ],
' => [    'adk  1       forward adk|b0474,
                                           []
                                         ],
          'agaS-kbaY-agaBCDI    6       forward agaB|b3138,agaC|b3139,
+agaD|b3140,agaI|b3141,agaS|b3136,kbaY|b3137,' => [
                                                                      
+                                          []
                                                                      
+                                        ],
' => [    'adiC 1       reverse adiC|b4115,
                                             []
                                           ],
' => [    'aes  1       reverse aes|b0476,
                                           []
                                         ],
' => [    'accBC        2       forward accB|b3255,accC|b3256,
                                                         []
                                                       ],
' => [    'add  1       forward add|b1623,
                                           []
                                         ],
' => [    'accD 1       reverse accD|b2316,
                                             []
                                           ],
' => [    'adrA 1       forward adrA|b0385,
                                             []
                                           ],
' => [    'adiA 1       reverse adiA|b4117,
                                             []
                                           ],
' => [    'aer  1       reverse aer|b3072,
                                           []
                                         ],
' => [    'acrEF        2       forward acrE|b3265,acrF|b3266,
                                                         []
                                                       ],
' => [    'acs-yjcH-actP        3       reverse acs|b4069,actP|b4067,y
+jcH|b4068,
                                                                      
+     []
                                                                      
+   ],
' => [    'abgR 1       forward abgR|b1339,
                                             []
                                           ],
' => [    'C0719        1       forward C0719|,
                                          []
                                        ],
' => [    'adiY 1       reverse adiY|b4116,
                                             []
                                           ],
' => [    'C0343-dbpA   2       forward C0343|,dbpA|b1343,
                                                          []
                                                        ],
          'manA' => [
                      [
                        'b1613'
                      ]
                    ],
' => [    'acrAB        2       reverse acrA|b0463,acrB|b0462,
                                                         []
                                                       ],
' => [    'C0067        1       forward C0067|,
                                          []
                                        ],
' => [    'adhE 1       reverse adhE|b1241,
                                             []
                                           ]
        };
[download]

I think you have tabs separating the fields instead of 4 spaces that the code somebody wrote is expecting, and unexpected carriage return characters at the end of lines. Changing it to

my @fields = split(' ', $_);
[download]

(or just my @fields = split;, since ' ' and $_ are what split defaults to) solves both problems.