#!/usr/bin/perl
use strict;
use warnings;
use Cwd;                      #Takes in the current path of the directory
use FileHandle;
my $cwd = getcwd();              #Takes in the current directory of files
my $opendir = "$cwd";               #Obtains the path of your current directory
my $treeFile = pop;
my %taxonomy = map { /(\S+)\s+(.+)/; $1 => $2 } <>;
push @ARGV, $treeFile;
my @file_name;
my @file;
my @directory = grep /tre$/, readdir DIR;  #assuming all your tree files have the tre as file extension
opendir (DIR, $opendir) or die $!;              #Opens the current directory, the path of all your files
my $scalar = scalar(@directory);                #Counting the number of files and printing it in the next line
for (my $i=0; $i<scalar(@directory); $i++){
my $name = $directory[$i];
print "The file read in: $name\n";
push @file_name,$name;
my $tmp = "$opendir/$directory[$i]";
open(FILE, $tmp) or die "Can't open $tmp\n";              #Reading the file and storing them in a string in the rep_line array
while ( <FILE> ) {
    $line = $_;
    $line =~ s/\b$_\b/$taxonomy{$_}/g for keys %taxonomy;
    #print $line;
    push @file,$line;
    }
}


mkdir "$cwd/Individual_tree_files"; 
for (my $i=0;$i<scalar(@file);$i++){
printer($file_name[$i],$file[$i]);                  #Calls the subroutine for printing to new files
}


sub printer { 
my @print_array = @_;
my $print_name = substr $print_array[0],1,-1;                           #Use a substring to grab the first part of the file name, modify accordingly
$print_name=~ s/\//_/g;
print "$print_name\n";
my $tree= "\.tre";
my $name_for_folder = "Individual_tree_files/";
my $name_for_file = "$name_for_folder$print_name$tree";                        #Creating the name for every output file
print "$name_for_file\n";
open(my $fh, '>',$name_for_file) or die "Could not open file '$name_for_file' $!";
 print $fh "$print_array[1]";                                                          #Printing the output file into the folder
 print "File for $print_name copied to Individual_tree_files\n";
 close $fh;
}