Given a mapping (in the form of a tab-delimited text file), collapse the mapping so that each key occupies a single line.

map-collapse.pl

#!/usr/bin/env perl

# Copyright (c) 2013, Daniel S. Standage <daniel.standage@gmail.com>
#
# input:  two columns of data in tab-delimited format, mapping from a key
#         (column 1) to a value (column 2);
# output: also two columns of data in tab delimited format, but all values
#         sharing the same key are printed on a single line; that is, each key
#         corresponds to a comma-separated list of associated values

use strict;

my %data;
while(<STDIN>)
{
  chomp;
  my @values = split(/\t/);
  $data{ $values[0] }->{ $values[1] } = 1;
}

foreach my $key(sort keys %data)
{
  my $valuelist = $data{$key};
  my @values = sort keys %$valuelist;
  my $valuestring = join(",", @values);
  printf("%s\t%s\n", $key, $valuestring);
}