#!/usr/bin/perl -w

# usage : perl sm_tophat.pl <read1 file> <read2 file>
# Sarah Maman - 2016
# Copyright (C) 2016 INRA
# 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 3 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, see <http://www.gnu.org/licenses/>.
#


use strict;
use File::Basename;
use Config::IniFiles;

my $cfg = Config::IniFiles->new( -file => "/path/to/PATH.ini" );
my $path = $cfg->val( 'workPath', 'FILEPATH_DEV' );
	
my $TOPHAT = $cfg->val( 'toolsPath', 'TOPHAT2_PATH' );
my $bowtie2build = $cfg->val( 'toolsPath', 'BOWTIE2_INDEXATION_PATH' );

my $lib                     = $ARGV[0];
my $input_read1             = $ARGV[1];
my $input_read2             = $ARGV[2];
my $reference_selector      = $ARGV[3];
my $input_reference         = $ARGV[4];
my $p                       = $ARGV[5];
my $r                       = $ARGV[6];
my $max_intron              = $ARGV[7];
my $output_bam              = $ARGV[8];
my $output_bed              = $ARGV[9];
my $output_unmapped_bam     = $ARGV[10];
my $zip                     = $ARGV[11];
my $gtf_cond                = $ARGV[12];
my $inputGTF                = $ARGV[13];


print STDOUT "REFERENCE: *$input_reference*\n\n";

my $cmd = ''; my $cmd2 = '';
my $poption ="",
my $roption ="";
my $max_intron_option ="";
my ($nb) = ($output_bam=~/galaxy_dataset_(\d+)\.\S+$/);
my $liboption="";
my $genome_index_base="";

if (!$lib eq ""){$liboption = "--library-type $lib";}
if (!$p eq ""){$poption = "-p $p";}
if (!$r eq ""){$roption = "-r $r";}
if (!$max_intron eq ""){$max_intron_option = "--max-intron-length $max_intron";}

my $gtfoption ='';
if (!$gtf_cond eq "F"){$gtfoption = "-G $inputGTF";}
else {$gtfoption ="";}

#Creation du repertoire de sortie des resultats
`cd $path/; mkdir $nb/; chmod -R 777 $nb/;`;

my $working_dir="$path/$nb/";
# if the Biologist has his own reference file
# generate the bowtie index for that reference
print STDOUT "reference_selector : *$reference_selector*\n\n";
if($reference_selector eq "history"){
	
	# copy your fasta file to the working directory
	`cp $input_reference "$working_dir/reference.fasta"`;
	chdir($working_dir) or die "system failed: chdir($working_dir) : $?"; 
	my $info=`pwd`;
	print STDOUT "INFO:Changed to working directory: $info \n ";
	
	# index the reference
	# get the "genome_index_base" ?
	$cmd = "($bowtie2build reference.fasta genome_index_base ) >& ./tophat.log 2>&1";
	
	#Info pour les biologistes
	print STDOUT "Tophat : \n\n $cmd \n\n ";
	system $cmd;
	
	# retrieve the new reference path
	$genome_index_base="$path/$nb/genome_index_base";
}
else{
	$genome_index_base=$input_reference;
}

print STDOUT "genome_index_base: *$genome_index_base*\n\n";

#Donner l extension fastq.gz si les fichiers sont zippes
if ($zip eq "YES"){
	
	print STDOUT "FASTQ files zipped ? $zip \n\n ";
	`cp $input_read1 $input_read1.fastq.gz ; `;
	`cp $input_read2 $input_read2.fastq.gz ; `;
	
	$cmd = "($TOPHAT -o '$path/$nb/' $poption $max_intron_option $roption $gtfoption $genome_index_base $input_read1.fastq.gz $input_read2.fastq.gz) >& ./tophat.log 2>&1";
	
	#Info pour les biologistes
	print STDOUT "Tophat : \n\n $cmd \n\n ";
	system $cmd;
}
else
{
	$cmd2 = "($TOPHAT -o '$path/$nb/' $liboption $poption $max_intron_option $roption $gtfoption $genome_index_base $input_read1 $input_read2) >& ./tophat.log 2>&1";
	
	#Info pour les biologistes
	print STDOUT "Tophat : \n\n $cmd2 \n\n ";
	system $cmd2;
}



if (! -e "$path/$nb/accepted_hits.bam")
{
print STDERR "BAM FILE NOT FOUND\n";
}
else
{
`mv "$path/$nb/accepted_hits.bam" $output_bam`;
}

if (! -e "$path/$nb/unmapped.bam")
{
print STDERR "unmapped.bam FILE NOT FOUND\n";
}
else
{
`mv "$path/$nb/unmapped.bam" $output_unmapped_bam`;
}

 
if (! -e "$path/$nb/junctions.bed")
{
print STDERR "JUNCTIONS BED FILE NOT FOUND\n";
}
else
{
`mv "$path/$nb/junctions.bed" $output_bed`;
}