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As for your questions, you can get a list of modules by querying CPAN's search facility. Here is a link with the search box filled in for you: Csv (116 hits). We also have a large number of threads at PerlMonks discussing CSV file parsing. Here is a Super Search query filled out to search for root nodes with "csv" in the title. Just press the search button and you will see a list of all of the nodes for the last year or so. You can also get to the Super Search screen by clicking on the link in the upper right corner of each PerlMonks page.

Best, beth

Update: added super search links.

Without proper post formatting it is hard to see what you want, but at a guess your input looks like this? :

ARL6IP2,298757,Hyperalgesia,MESH:D006930
ARL6IP2,298757,Liver Diseases,MESH:D008107
ARL6IP2,298757,"Liver Failure, Acute",MESH:D017114
ARL6IP2,298757,Liver Neoplasms,MESH:D008113
CCL22,6367,Esophageal Neoplasms,MESH:D004938
CCL22,6367,Fatty Liver,MESH:D005234
CCL22,6367,Fetal Growth Retardation,MESH:D005317
CCL22,6367,Fever,MESH:D005334
[download]

In which case you need to build a hash based on your unique keys (gene names by the look of it). Hashes are perfect for dealing with data that is organised by unique identifiers.
I would probably go about it like this :

• open the file and read it line by line
• parse each csv formatted line into the relevant parts
• add the third and fourth columns (diease and MeSH term) to an array of arrays referenced by a unique hash key ( the first column )
• when the file in finished, close it
• open an Spreadsheet::WriteExcel sheet or a Spreadsheet::DataToExcel (maybe simpler?) and write out to it

use warnings;
use strict;

## for parsing the CSV
use Text::CSV::Simple;
## for writing to excel
use Spreadsheet::WriteExcel;

my $datafile = ... the one you gave earlier ...

# Only capture feilds of interest
my $parser = Text::CSV::Simple->new;
$parser->want_fields(1, 3, 4, );
my @data = $parser->read_file($datafile);
## data is now read in (if you file is really big, you can do this on-
+the-fly too)
my %hash = (); ## for storing collated data
foreach @data{
  ## store terms acording to unique id
  push @{ $hash{$_->[0]}->[0] }, $_->[1]; ## disease term stored in an
+ array
  push @{ $hash{$_->[0]}->[1] }, $_->[2]; ## MeSH term also stored in 
+an array
}

## now print out data
# Create a new workbook called simple.xls and add a worksheet
my $workbook  = Spreadsheet::WriteExcel->new('simple.xls');
my $worksheet = $workbook->add_worksheet();

# The general syntax is write($row, $column, $token). Note that row an
+d
# column are zero indexed
my $row = 0;
for my $key ( keys %hash ){
  $worksheet->write($row, 0, $key); ## id
  $worksheet->write($row, 1, ( join ', ', @{ $hash{$key}->[0] } )); ##
+ diseases
  $worksheet->write($row, 2, ( join ', ', @{ $hash{$key}->[1] } )); ##
+ MeSH

  ++$row; ## move to the next row
}
print "$0 completed : ".(scalar(localtime))."\n";
[download]

I haven't tested this, but hopefully it will give you some ideas.

use warnings;
use strict;

use Text::xSV;

my $csv = Text::xSV->new(fh => *DATA);

my %res;

while (my $row = $csv->get_row()) {
    my $index = shift @$row;
    $res{$index}->{id} = shift @$row;
    push @{$res{$index}->{desc}}, shift @$row; 
    push @{$res{$index}->{mesh}}, shift @$row; 
}

my $xls = Text::xSV->new();

$xls->print_row($_, join(q/,/, @{$res{$_}->{desc}}), join(q/,/, @{$res
+{$_}->{mesh}})) for keys %res;

__DATA__
ARL6IP2,298757,Hyperalgesia,MESH:D006930
ARL6IP2,298757,Liver Diseases,MESH:D008107
ARL6IP2,298757,"Liver Failure, Acute",MESH:D017114
ARL6IP2,298757,Liver Neoplasms,MESH:D008113
CCL22,6367,Esophageal Neoplasms,MESH:D004938
CCL22,6367,Fatty Liver,MESH:D005234
CCL22,6367,Fetal Growth Retardation,MESH:D005317
CCL22,6367,Fever,MESH:D005334
[download]

$ perl tst.pl
CCL22(Esophageal Neoplasms,Fatty Liver,Fetal Growth Retardation,Fever)
+,(MESH:D004938,MESH:D005234,MESH:D005317,MESH:D005334)
ARL6IP2(Hyperalgesia,Liver Diseases,Liver Failure, Acute,Liver Neoplas
+ms),(MESH:D006930,MESH:D008107,MESH:D017114,MESH:D008113)
[download]

1. Modify my $xls = Text::xSV->new(); to read my $xls = Text::xSV->new(filename => 'foo.xls.csv'); - thus facilitating the saving of the translated file
2. Use Win32::OLE to start an Excel session to import the generated file (foo.xls.csv) and save it to the target .xls filename - it's a bit hard to demonstrate on a Linux box (yes, I have no Windoze:-)), so any amount of google hits are there provide guidance for this step.

Update 1:

Oops, I really ought to have looked _closely_ at the results - missing delimiter between the 2 lists - now corrected

Update 2:

Having re-read your OP, I see that the brackets were merely placeholders indicating column/field limits, so bearing this in mind, I simplified the snippet (to utilise the print_row() call) and re-structure the print loop.

As the other responders noted, I also am not entirely sure what you're looking for. But following the general trend regarding what you're after, here is another strategy for handling what I think you're looking for.

The input file that I used to test the above code looks like this:

With that input and the above code, the output to the terminal looks like the following:

1: (CCL22),(Esophageal Neoplasms,Fatty Liver,Fetal Growth Retardation,
+Fever),(MESH:D004938,MESH:D005234,MESH:D005317,MESH:D005334)
2: (ARL6IP2),(Hyperalgesia,Liver Diseases,"Liver Failure, Acute",Liver
+ Neoplasms),(MESH:D006930,MESH:D008107,MESH:D017114,MESH:D008113)
[download]

As suggested by the other responders, this code uses a hash as the mechanism for storing the various codes (e.g., "ARL6IP2" or "CCL22"). Each entry in the has stores a reference to an array which, itself contains references to two other arrays. One of those two arrays is an array of what I designate as the @diseases (e.g., "Hyperalgesia" or "Liver Failure, Acute" associated with each $code) and the other is an array of what I designate as @meshes (i.e., the various "MESH:D006930" type of stuff associated with each $code).

The one perhaps odd looking construct in the script is:

$codes{$code} = [[@diseases],[@meshes]];
[download]

The use of the square brackets in the interior are to ensure that all of the entries in the hash don't point to the exact same array. The use of the square brackets in this way is the usual recommended way to ensure that one doesn't continually point to the same data structure.

I hope this helps show another way to do it.