#!/usr/bin/perl
use strict;
use DateTime;
use File::Copy;
use File::Find;
use File::stat;
use Time::localtime;


my $now = DateTime->now(time_zone => 'floating');
my $yesterday = $now->subtract(days=>1);
my $year = $yesterday->year;
my $month = $yesterday->month;
my $month_abbr = uc($yesterday->month_abbr);# uppercase string chars
my $day = $yesterday->day;
my $year_abbr = substr "$year",2,2;
my $mdy = $now->strftime("%m-%d-%y");

print "$year\t$year_abbr\t$month\t$month_abbr\t$day\n";
# location of files to be processed.
my $root="/Users/mgavi.brathwaite/Desktop/BioinfDev/SequenceAssemblyProject/Sequencing_Results/RESULTS $year/New Version/Amanda Li/$month_abbr "."$year";
print "$root\n";
# location of maid directories
my $komp_dir ="/Users/mgavi.brathwaite/Desktop/BioinfDev/SequenceAssemblyProject/KOMP";
my %files();
find(\&wanted, $root);

#check the arrays in the hash looking for maids with 4 files
foreach my $k (keys(%files)){
  #get the array from the array reference.
  #See how the reference gets in the has below.
  my @arr=@{$files{$k}};   
   #skip unless we have 4 files in the array                      
  next unless ( scalar my @array) == 4;  
  #look for KOMP maid directory we want to copy to
  #glob dirs with a regex something like /$k\D/ - lets call it $KOMP_dir
  $komp_dir = maid_dirs($k);
  #Create the sequencing sub dir under $KOMP_dir
  #so now KOMP_dir=KOMP_dir+"/sequencing"
  mkdir $komp_dir."/sequencing",0755;
  $komp_dir=$komp_dir."/sequencing/";
  #now iterate through the array, copying the files.  You know the maid number ($k)
 foreach my $f (@arr){ 
   copy("$f","$komp_dir/$f")  or die "Copy failed: $!";
 } 
	#do_phred_phrap($komp_dir);
}
=for
  sub do_phred_phrap{
	my $dir=shift;
	
  }
=cut



################################ Subroutines ################################

sub wanted {
	my $targetfile =  $File::Find::name;
	return if $targetfile =~ /xls$/;
	# -M	Script start time minus file modification time, in days.
	# skip unless mod date is less than one day ago
	return if (-M  $targetfile > 1.0);
	#determine maid number
	(my $maid = $1) = $targetfile=~ /.*\/(\d*)/; 
	  my @arr=null;
	  if ($files{$maid}){
	   @arr=@{$files{$maid}};  
	  }else{
	    @arr=[];
	  }
	# IMPORTANT!!!!  $targetfile should be the full path to the file so
	# you don’t have to figure out how to recreate it when copying
	  push @arr, $targetfile;
	#set the array reference as the hash value. 
	#You get the array back with my code above in the ‘if’ statement.  
	  $files{$maid}=\@arr;   
	                        
}


#you will pass in the maid number as an argument
sub maid_dirs{
    my $maid=shift;
    @dirs =   glob("/Users/mgavi.brathwaite/Desktop/BioinfDev/SequenceAssemblyProject/KOMP/*");
    foreach $komp_dir(@dirs) {
        if (-d $komp_dir){
            if ($komp_dir=~/.*\/$maid\D/){
                return $komp_dir;
            }
        }
    }    
}
print "\ndone\n";