#!/usr/bin/perl

#############################################################################
#extract_genes_from_TIGR_XML.pl
#Extracting coordinates from TIGR's XML annotation files.
#Copyright (c) 2005 Diego Mauricio Riaño Pachón
#http://www.geocities.com/dmrp.geo
#
#This script requires XML::Simple and the TIGRXMLLIB available 
#from TIGR's web site ftp://ftp.tigr.org/pub/data/a_thaliana/ath1/XML_TOOLS/
#
#This program is free software; you can redistribute it and/or
#modify it under the terms of the GNU General Public License
#as published by the Free Software Foundation; either version 2
#of the License, or (at your option) any later version.
#
#This program is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#GNU General Public License for more details.
#
#You should have received a copy of the GNU General Public License
#along with this program; if not, write to the Free Software
#Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
#############################################################################

use lib ("TIGRXMLLIB");
use TIGR_XML_parser;
use Gene_obj;
use strict;
use warnings;
use Getopt::Long;
#use diagnostics;

my $version=1.0;
my $license="";
my $help="";
my @files=();

GetOptions(
    'file|f=s' => \@files,
    'license|l' => \$license,
    'help|h|?' => \$help
);

if (@files){

foreach my $file(@files){
    my $output=$file;
    $output=~s/\.xml$/\.tbl/;
    open OUT, ">$output";
    my $TIGRparser=new TIGR_XML_parser();
    my $pwd=`pwd`;
    chomp $pwd;
    unless ($file=~/\//){
	$file="$pwd/$file";
    }
    print STDERR $file."\n";
    $TIGRparser->capture_genes_from_assembly_xml("$file");
    my @genes=$TIGRparser->get_genes();
    print OUT "TYPE\tLOCUS\tMODEL\tMODEL_END5\tMODEL_END3\tGENE_END5\tGENE_END3\n";
    foreach my $gene(@genes){
	$gene->refine_gene_object();
        #From Gene_obj.pm: this are the different gene types: protein-coding|rRNA|snoRNA|snRNA|tRNA
        #I will keep separated protein-coding genes from RNA genes
        #additionaly pseudogenes are annotated as proteins coding genes, then an additional step is needed to take them apart.
        #I added a tag at the beginning of each row to distinguish between protein-coding, pseudogene and RNAgene
	if($gene->{gene_type}=~/^protein-coding$/){
	    if ($gene->{is_pseudogene}==0){
		my $model=$gene->{model_pub_locus};
		my ($modelend5,$modelend3)=$gene->get_model_span();
		my ($genend5,$genend3)=$gene->get_gene_span();
		print OUT "protein-coding\t".$gene->{pub_locus}."\t$model\t$modelend5\t$modelend3\t$genend5\t$genend3\n";
		my @isoforms=$gene->get_additional_isoforms();
		if (@isoforms){
		    foreach my $isoform(@isoforms){
			my $model=$isoform->{model_pub_locus};
			my ($modelend5,$modelend3)=$isoform->get_model_span();
			my ($genend5,$genend3)=$gene->get_gene_span();
			print OUT "protein-coding\t".$gene->{pub_locus}."\t$model\t$modelend5\t$modelend3\t$genend5\t$genend3\n";
		    }
		}
	    }
	    else{
		my $model=$gene->{model_pub_locus};
		my ($modelend5,$modelend3)=$gene->get_model_span();
		my ($genend5,$genend3)=$gene->get_gene_span();
		print OUT "pseudogene\t".$gene->{pub_locus}."\t$model\t$modelend5\t$modelend3\t$genend5\t$genend3\n";
		my @isoforms=$gene->get_additional_isoforms();
		if (@isoforms){
		    foreach my $isoform(@isoforms){
			my $model=$isoform->{model_pub_locus};
			my ($modelend5,$modelend3)=$isoform->get_model_span();
			my ($genend5,$genend3)=$gene->get_gene_span();
			print OUT "pseudogene\t".$gene->{pub_locus}."\t$model\t$modelend5\t$modelend3\t$genend5\t$genend3\n";
		    }
		}
	    }
	}
	else{
	    my ($genend5,$genend3)=$gene->get_gene_span();
	    print OUT "RNAgene\t".$gene->{pub_locus}."\t\t$genend5\t$genend3\t$genend5\t$genend3\n";
	}
    }
}
}
elsif($license){
    &license;
}
else{
    &usage;
}
sub usage{
    print STDERR "$0 version $version, Copyright (C) 2005 Diego Mauricio Riaño Pachón\n";
    print STDERR "$0 comes with ABSOLUTELY NO WARRANTY; for details type `$0 -l'.\n";
    print STDERR "This is free software, and you are welcome to redistribute it under certain conditions;\n";
    print STDERR "type `$0 -l' for details.\n";
    print STDERR <<EOF;
NAME
    extract_genes_from_TIGR_XML.pl   Extracting coordinates from TIGR's XML annotation files

USAGE
    extract_genes_from_TIGR_XML.pl -f file1.xml -f file2.xml -f file3.xml

OPTIONS
    --file,    -f   TIGR's XML file with annotation for assembly/pseudomolecule
    --help,    -h    This help
    --license, -l    License.

EOF
    exit;
}

sub license{
    print STDERR <<EOF;

Copyright (C) 2005 Diego Mauricio Riaño Pachón
http://www.geocities.com/dmrp.geo
e-mail: diriano\@gmail.com

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
EOF
exit;
}