use strict;
use warnings;

# Create a test file
open outFile, ">", "file1.txt";
print outFile <<end;
rabbit 1
hen    0
pig    2
cow    2
sheep  5
end
close outFile;

#Sample code
open inFile, "<", "file1.txt" or die "Unable to read file1.txt. $!";
my @lines = <inFile>;
close inFile;

my %animals;

# build a hash keyed by animal with the count as value
map {/(\w+)\s+(\d+)/; $animals{$1}=$2} @lines;

# Production code would use file2 rather than DATA
while (<DATA>)
  {
  /(\w+)/; #Assume animal is always the first thing on the line

  # Bump animal count - creates new entry if new animal
  ++$animals{$1} if defined $1;
  }

open outFile, ">", "file1.txt";
for (@lines)
  {
  /(\w+)/;
  printf outFile "%-6s %d\n", $1, $animals{$1};
  $animals{$1} = 0; # Tag as printed
  }

#add any new animals to the end of the file
for (keys %animals)
  {
  next if ! $animals{$_};
  printf outFile "%-6s %d\n", $_, $animals{$_};
  }

close outFile;

__DATA__
rabbit feed 10kg used on 21/10/2005 by consumer1
cow feed 100kg used on 11/11/2005 by consumer1
sheep feed 50kg used on 24/11/2005 by consumer3
[download]

Creates a file containing:

rabbit 2
hen    0
pig    2
cow    3
sheep  6
[download]