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

my ($name, $output_dir, $project) = @ARGV;
die "useage:perl $0 codes_dir name output_dir project" unless @ARGV == 4;

my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/";
open INFO, "$public_path/info.csv";
<INFO>;
my @promoter;
while (<INFO>) {
    chomp;
    my @line = split(/\t/, $_);
    if ($line[0] eq $project) {
        if ($line[4] ne "NA") {
            @promoter = split(/\//, $line[4]);
            open PRMT, ">$output_dir/mutation/${name}.target.promoter.txt";
        }
    }
}

my @prmt;

open IN2, "$output_dir/mutation/${name}.snp.indel.Somatic.annoall.hg19_multianno.txt";
<IN2>;
while (<IN2>) {
    chomp;
    my @line = split(/\t/, $_);

    if (@promoter and grep {$line[6] eq $_} @promoter) {
        if ($line[5] =~ /UTR3|upstream/ and $line[17] < 0.01
            and $line[18] < 0.01 and $line[19] < 0.01 and $line[20] < 0.01 and $line[23] < 0.01 and $line[28] < 0.01 and $line[32] < 0.01) {
            my @var = split(/;/, $line[9]);
            my $freq = (split(/:/, $line[-2]))[5];
            my $dp4 = join(",", (split(/:/, $line[-2]))[2, 4, -1]);
            my $predict_benign = 0;
            $predict_benign++ if ($line[50] eq "N" or $line[50] eq "P");
            $predict_benign++ if $line[56] eq "T";
            $predict_benign++ if $line[64] eq "T";
            if ($line[6] eq 'TERT') {
                push @prmt, join("\t", @line[0 .. 9], $freq, $dp4, $predict_benign, @line[10, 11, 16, 18, $#line])
                    if (($line[1] eq '1295228' and $line[4] eq 'A') or ($line[1] eq '1295250' and $line[4] eq 'A'));
            }
        }
    }
}

if (@prmt) {
    print PRMT join("\t", @head[0 .. 9]), "\tFreq", "\tDP-AD-DP4", "\tpredict_benign(MutationTaster/FATHMM/MetaSVM)\t", join("\t", @head[10, 11, 16, 18]), "\tSTR", "\n";
    print PRMT join("\n", @prmt) . "\n";
}