#!/usr/bin/perl
use strict;
use File::Copy;

=for
Create a hash to match the primer files with the maid folder.
When a match occurs, copy it to the maid folder. Next
create a new folder and populate it with the files to be 
processed by the sequence assembler.

path to sequence files:
"/Data/Sequencing_Results/RESULTS 2009/New Version 2009/Amanda Li";
=cut
my %fields_hash;
$lt_vec_seq = "/Data/Velocigene/Production Design/KOMP"; # Location of the maid files
$seq_results = "/Data/Velocigene/Production Design/KOMP/SequenceAssemblies";

# create hash consisting of maids as keys and sequence files as values
sub seq_assembly{
# create a hash with maid folders as keys and the primer seq files as values
	my %sequence_hash;
	$sequence_hash{$lt_vec_seq} = $seq_results;
	my @sorted_keys = sort { $a <=> $b || $b cmp $a } keys %sequence_hash;
	foreach my $key (@sorted_keys) {
	# Could use some direction concerning copying the $seq_results(where files
	# exist) into $lt_vec_seq(directory)
		copy(); 
	}
}