#!/usr/bin/perl -w
use strict;
use warnings;
use ScriptManager;
use Getopt::Long;
use File::Basename qw(basename);
my $BEGIN_TIME=time();

my ($out_file,$gtf,$all_gene);
GetOptions(
	"help|?" =>\&USAGE,
	"o:s"=>\$out_file,
	"g:s"=>\$gtf,
    "a"=>\$all_gene
) or &USAGE;
&USAGE unless ($gtf  and @ARGV);
$out_file ||="Annotation.xls";

my @heads=("Chromosome","Start Site","End Site","Direction","Length","Name",@ARGV);

open F,$gtf or die $!; 
my %gene;
open O,">tmp_gene_exon.bed" or die $!;
while (<F>) {
    chomp;
	next if(/^#/);
    if(/\tgene\t/){
        if(! $all_gene){
            next unless /protein_coding/;
        }
        my @line=split/\t/;
        my ($gene_name)=$line[8]=~/gene_name \"([^\"]+)\"/;
        my ($gene)=$line[8]=~/gene \"([^\"]+)\"/;
		my ($Name)=$line[8]=~/Name \"([^\"]+)\"/;
		my ($locus_tag)=$line[8]=~/locus_tag \"([^\"]+)\"/;
		my $last_name=$gene_name||$Name||$gene||$locus_tag;
        my ($gene_id)=$line[8]=~/gene_id \"([^\"]+)\"/;
        $gene{$gene_id}{"Chromosome"}=$line[0];
        $gene{$gene_id}{"Start Site"}=$line[3];
        $gene{$gene_id}{"End Site"}=$line[4];
        $gene{$gene_id}{"Direction"}=$line[6];
        $gene{$gene_id}{"Name"}=$last_name;
    }
	next unless(/\texon\t/);
	if(/\texon\t(\d+)\t(\d+).+gene_id \"([^\"]+)\"/){
		my $start=$1-1;
		my $end=$2;
		my $geneID=$3;
        print O join("\t",$geneID,$start,$end)."\n";
	}
}
close F;
close O;
`bedtools sort  -i  tmp_gene_exon.bed > tmp_gene_exon.sort.bed && bedtools merge -i tmp_gene_exon.sort.bed  >tmp_no_overlap.bed`;
open I, "tmp_no_overlap.bed" or die $!;
while(<I>){
    chomp;
    next if /^\s*$/;
    my @line=split/\t/;
    $gene{$line[0]}{"Length"}+=($line[2]-$line[1]);
}
close I;
`rm -f tmp_gene_exon.bed tmp_gene_exon.sort.bed tmp_no_overlap.bed`;

foreach my $anno_file (@ARGV){
    open IN,$anno_file or die $!;
    while(<IN>){
        chomp;
        next if(/^\s*$/ || /^#/);
        my @line=split/\t/;
        if($gene{$line[0]}){
            $gene{$line[0]}{$anno_file}=$line[1];
        }
    }
    close IN;
}

open OUT,">$out_file" or die $!;
print OUT join("\t","Gene ID",@heads)."\n";
foreach my $g (sort keys %gene){
    $gene{$g}{"Length"}=$gene{$g}{"End Site"} - $gene{$g}{"Start Site"} + 1 if( ! $gene{$g}{"Length"} );
    print OUT join("\t","$g",map { $gene{$g}{$_} || "-" } @heads ),"\n" if($gene{$g}{"Start Site"});
}
close OUT;

print STDOUT "\nDone. Total elapsed time : ",time()-$BEGIN_TIME,"s\n";

sub USAGE {
        my $usage=<<"USAGE";
Usage:perl $0 -g reference.gtf -o Annotation.xls GO KEGG eggNOG ...
Description:Calculate gene exon length and Megre GO KEGG NR eggNOG NR Swissprot 
Options:
	-o <outfile>	output Annotation file default "Annotation.xls"
	-g <gtf>	reference genome gtf file
    -a  all gene ;
	-h help

USAGE
        print $usage;
        exit;
}
################################################################################################################

sub GetTime {
	my ($sec, $min, $hour, $day, $mon, $year, $wday, $yday, $isdst)=localtime(time());
	return sprintf("%4d-%02d-%02d %02d:%02d:%02d", $year+1900, $mon+1, $day, $hour, $min, $sec);
}

################################################################################################################