#!/usr/bin/perl

use strict;
use warnings;
use File::Copy;

# This script reads all provisional studies on datahub and does the following fixes:
# 1. Checks if the sample_type value corresponds to the tcga barcode else fixes it in place.
# 2. Corrects the sample_type_id col
# 3. Changes the PRIMARY_SITE, METASTATIC_SITE and TUMOR_TISSUE_SITE attribute headers and descriptions to patient level attributes PRIMARY_SITE_PATIENT, METASTATIC_SITE_PATIENT and SITE_OF_TUMOR_TISSUE

my %bar_codes = ('01' => 'Primary', '02' => 'Recurrent', '03' => 'Primary', '05' => 'Primary', '06' =>  'Metastatic', '07' =>  'Metastatic', '11' => 'Normal', '12' => 'Normal');
my %sampletypeids = ('01' => '1', '02' => '2', '03' => '3', '05' => '5', '06' =>  '6', '07' =>  '7', '11' => '11', '12' => '12');
my $path = "/Users/rmadupuri/GitHub/datahub/public";
my @dirs;
opendir(D,$path);
while(my $dir = readdir(D))
{
	next if $dir =~ /^\./;
	if($dir =~ /._tcga$/) # For provisional studies
	{
		push(@dirs,$dir);
	}
}
closedir(D);


# correct the sample types
foreach(@dirs)
{
	my $dirname = $_;
	my $dirpath = $path."/".$_;

	if (-d $dirpath)
	{
		opendir(H,$dirpath);
		while(my $file = readdir(H))
		{
			if($file =~ /.data.sample./)
			{

				my $filepath = $dirpath."/".$file;
				open(FH,"<$filepath") or die("can't open the file");
				my $file_cont = "";
				my $pat_col;
				my $sam_col;
				my $sam_typeid_col;
				while(my $line = <FH>)
				{
					if($line =~ /^#/)
					{
						$file_cont .= $line;
						next;
					}
					elsif($line =~ /^PATIENT_ID/ || $line =~ /^SAMPLE_ID/)
					{
						$file_cont .= $line;
						my @arr = split("\t",$line);
						for(my $i=0;$i < scalar(@arr);$i++)
						{
							if($arr[$i] eq "SAMPLE_ID"){ $pat_col = $i};
							if($arr[$i] eq "SAMPLE_TYPE"){ $sam_col = $i};
							if($arr[$i] eq "SAMPLE_TYPE_ID"){ $sam_typeid_col = $i};
						}
					}
					else
					{
						my @arr1 = split("\t",$line);

						my @s_c = split("-",$arr1[$pat_col]);
						my $sam_code = $s_c[scalar(@s_c)-1];

						if($arr1[$sam_col] ne $bar_codes{$sam_code})
						{
							if($arr1[$sam_typeid_col] ne $sampletypeids{$sam_code})
							{
								$arr1[$sam_typeid_col] = $sampletypeids{$sam_code};
							}
							#print $dirname."\t".$arr1[$pat_col]."\t".$arr1[$sam_col]."\t".$bar_codes{$sam_code}."\n";
							$arr1[$sam_col] = $bar_codes{$sam_code};
							my $str = join("\t",@arr1);
							$file_cont .= $str;

						}
						else
						{
							if($arr1[$sam_typeid_col] ne $sampletypeids{$sam_code})
							{
								$arr1[$sam_typeid_col] = $sampletypeids{$sam_code};
							}
							my $str = join("\t",@arr1);
							$file_cont .= $str;
						}
					}

				}
				close(FH);
				unlink($filepath);

				open(NF,">$filepath")	or die();
				print NF $file_cont;
			}


		}
	}
}



# change the patient attribute names
foreach(@dirs)
{
	my $dirname = $_;
	my $dirpath = $path."/".$_;

	if (-d $dirpath)
	{
		opendir(H,$dirpath);
		while(my $file = readdir(H))
		{

			if($file =~ /.data.patient./)
			{

				my $ps_col = -1;
				my $ms_col = -1;
				my $tts_col = -1;
				my $display_line;
				my $comments = "";
				my $header;
				my $file_cont = "";

				my $filepath = $dirpath."/".$file;
				open(FH,"<$filepath") or die("can't open the file");

				my $c=1;
				while(my $line = <FH>)
				{
					if($line =~ /^#/)
					{
						if($c == 1)
						{
							$display_line = $line;
							$c++;
						}
						else
						{
							$comments .= $line;
						}
					}
					elsif($line =~ /^OTHER_PATIENT_ID/)
					{
						$header = $line;
						my @arr = split("\t",$line);
						for(my $i=0;$i < scalar(@arr);$i++)
						{
							if($arr[$i] eq "PRIMARY_SITE"){ $ps_col = $i};
							if($arr[$i] eq "METASTATIC_SITE"){ $ms_col = $i};
							if($arr[$i] eq "TUMOR_TISSUE_SITE"){ $tts_col = $i};
						}
					}
					else
					{
						$file_cont .= $line;
					}
				}
				my @com_line = split("\t",$display_line);
				if($ps_col != -1){ $com_line[$ps_col] = "Patient Primary Tumor Site" };
				if($ms_col != -1){ $com_line[$ms_col] = "Patient Metastatic Sites" };
				if($tts_col != -1){ $com_line[$tts_col] = "Tumor Tissue Site" };
				my $new_disp_line = join("\t",@com_line);

				my @he_line = split("\t",$header);
				if($ps_col != -1){ $he_line[$ps_col] = "PRIMARY_SITE_PATIENT" };
				if($ms_col != -1){ $he_line[$ms_col] = "METASTATIC_SITE_PATIENT" };
				if($tts_col != -1){ $he_line[$tts_col] = "SITE_OF_TUMOR_TISSUE" };
				my $new_head_line = join("\t",@he_line);

				close(FH);

				unlink($filepath);

				open(NF,">$filepath")	or die();

				print NF $new_disp_line.$comments.$new_head_line.$file_cont;

			}

		}
	}
}