#!/usr/bin/perl
use strict;
use warnings;

my ($output_dir,$cancer_type)=@ARGV;
die "useage:perl $0 output_dir cancer_type" unless @ARGV==2;

my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase";

print "Indication药物注释使用路径：$database_path\n";

open OUT,">$output_dir/mutation/indication.txt";
print OUT "基因\t检测内容\t检测情况\t肿瘤类型\n";
##本癌种FDA/NMPA/NCCN批准基因检测
=pod
##疾病翻译信息
open DIS,"/dataseq/jmdna/codes/reportbase/cancer_type.txt";
my (%dis,%dis2);
<DIS>;
while(<DIS>){
	chomp;
	my @line=split(/\t/);
	$dis{lc$line[0]}=$line[1];
	push @{$dis2{$line[3]}},$line[0];
	push @{$dis2{$line[4]}},$line[0];
}
=cut

open DIS,"/dataseq/jmdna/codes/reportbase/oncotree.cancertype.20230801.txt";
<DIS>;
my (%dis,@id,%dis2);
while(<DIS>){
	chomp;
	my @line=split(/\t/);
	$dis{lc$line[2]}=$line[3];
	$dis{lc$line[4]}=$line[5];
	push @{$dis2{$line[0]}},lc$line[2];
	push @{$dis2{$line[0]}},lc$line[4];
	push @id,$line[0];
}
foreach my $ID($cancer_type){
        my @family;
        my @ids=split("",$ID);
        for (my $i=1;$i<@ids;$i=$i+2){
                push @family,join("",@ids[0..$i]);
        }
        push @family,(grep{/^$ID/}@id);
        foreach my $t(@family){
                push @{$dis2{$ID}},@{$dis2{$t}};
        }
}
foreach my $key(keys(%dis2)){
	my %uniq;
	@{$dis2{$key}}=grep{++$uniq{$_}<2}@{$dis2{$key}};
}

##靶向用药信息
open THERAPY,"$database_path/targetTherapy.txt";
 <THERAPY>;
my %therapy;
my %cancer;
while(<THERAPY>){
	chomp;
	my @line=split("\t");
	if($line[9] eq 'V' and $line[14] eq 'A' and (grep{lc$line[2] eq lc$_}@{$dis2{$cancer_type}}) and $line[0]!~/,/){
		push @{$cancer{$line[0]}},$dis{lc$line[2]} if !(grep{$_ eq $dis{lc$line[2]}}@{$cancer{$line[0]}});
		if($line[1]=~/fusion/i){
			push @{$therapy{$line[0]}},'融合' if !(grep{$_ eq '融合'}@{$therapy{$line[0]}});
		}elsif($line[1] eq "Deletion" or $line[1]=~ /Amplification/){
			push @{$therapy{$line[0]}},'扩增' if !(grep{$_ eq '扩增'}@{$therapy{$line[0]}});
		}else{
			push @{$therapy{$line[0]}},'突变' if !(grep{$_ eq '突变'}@{$therapy{$line[0]}});;
		}
	}
}

for my $gene(sort keys %therapy){
	print OUT "$gene\t",join("/",@{$therapy{$gene}}),"\t未检出变异\t",join("/",@{$cancer{$gene}}),"\n";
}