#!/usr/bin/perl

use strict;

use warnings;

# Author: Liu hualin

# Date: Oct 13, 2021

# Download modules

# 记录一个深坑，程序默认在 module 的路径前加了一个 "./module" 路径，因此，虽然程序安装的过程中自动下载了 modules，然而我们并没有办法调用它们，只能重新下载。

# 以下代码在当前目录下创建了 module 目录，并下载 modules，然后将其存到 module 目录中。

system("mkdir -p module");

system("curl -o TTSS_STD-2.0.2.jar https://depot.galaxyproject.org/software/TTSS_STD/TTSS_STD_2.0.2_src_all.jar");

system("curl -o TTSS_ANIMAL-1.0.1.jar https://depot.galaxyproject.org/software/TTSS_ANIMAL/TTSS_ANIMAL_1.0.1_src_all.jar");

system("curl -o TTSS_PLANT-1.0.1.jar https://depot.galaxyproject.org/software/TTSS_PLANT/TTSS_PLANT_1.0.1_src_all.jar");

system("curl -o TTSS_STD-1.0.1.jar https://depot.galaxyproject.org/software/TTSS_STD/TTSS_STD_1.0.1_src_all.jar");

system("mv -f TTSS_STD-2.0.2.jar TTSS_ANIMAL-1.0.1.jar TTSS_PLANT-1.0.1.jar TTSS_STD-1.0.1.jar module");

# Predict one by one

my @faa = glob("*.faa");

foreach  (@faa) {

	$_=~/(.+).faa/;

	my $out = $1 . ".T3";

	system("effectivet3 -f $_ -m TTSS_STD-2.0.2.jar -t selective -o $out -q");

}

# information aggregation

my (%hash, %strain);

my $line_num = 0;

open T3, ">T3SS.txt" || die;

print T3 "Strain\tId\tDescription\tScore\tis secreted\tProtein sequences\n";

my @t3 = glob("*.T3");

foreach my $t3 (@t3) {

	$t3=~/(.+).T3/;

	my $str = $1;

	my $faa = $1 . ".faa";

	$strain{$str}++;

	my %temp;

	# Save ID and Sequence to %temp

	open FAA, "$faa" || die;

	local $/ = ">";

	<FAA>;

	while (<FAA>) {

		chomp;

		my ($header, $seq) = split (/\n/, $_, 2);

		$header=~/(\S+)/;

		my $id = $1;

		$seq=~s/[\r\n]+//g;

		$temp{$id} = $seq;

	}

	close FAA;

	local $/ = "\n";

	open IN, "$t3" || die;

	<IN>;

	while (<IN>) {

		chomp;

		if (!/^#/) {

			my @lines = split /\;/;

			if ($lines[3] eq "true") {

				$line_num++;

				print T3 "$str\t" . join("\t", @lines) . "\t" . $temp{$lines[0]} . "\n";

				$hash{$str}{true}++;

			}else {

				$hash{$str}{false}++;

			}

		}

	}

	close IN;

}

close T3;

if ($line_num > 1) {

	open T3NUM, ">T3SS.num" || die;

	print T3NUM "Strain\tTotal sequences\tT3S effective true\tT3S effective false\n";

	foreach  (sort keys %strain) {

		if ($hash{$_}{true} && $hash{$_}{false}) {

			my $total = $hash{$_}{true} + $hash{$_}{false};

			print T3NUM $_ . "\t" . $total . "\t" . $hash{$_}{true} . "\t" . $hash{$_}{false} . "\n";

		}elsif ($hash{$_}{true}) {

			$hash{$_}{false} = 0;

			my $total = $hash{$_}{true} + $hash{$_}{false};

			print T3NUM $_ . "\t" . $total . "\t" . $hash{$_}{true} . "\t" . $hash{$_}{false} . "\n";

		}else {

			$hash{$_}{true} = 0;

			my $total = $hash{$_}{true} + $hash{$_}{false};

			print T3NUM $_ . "\t" . $total . "\t" . $hash{$_}{true} . "\t" . $hash{$_}{false} . "\n";

		}

	}

	close T3NUM;

}

system("mkdir -p T3SS_result");

system("mv *.T3 T3SS.num T3SS.txt T3SS_result");

perl run_effectiveT3.pl