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

Maybe it would go something like this :

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.

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