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#!/usr/bin/perl -w

# usage : perl sm_STAR.pl <read1.fastq.gz> <read2.fastq.gz>
# 10/02/2014 - Wrapper du traitement des données RNAseq
# Sarah Maman
# Copyright (C) 2014 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 Getopt::Long;
use lib "$ENV{'MY_GALAXY_DIR'}";
use GalaxyPath;

my $cfg = GalaxyPath->new( -file => $ENV{"GALAXY_CONFIG_FILE"});
my $PATH = $cfg->my_path( 'workPath', 'MYWORKSPACE' );
my $STAR = $cfg->my_path( 'toolsPath', 'STAR_PATH' );



my $Nthreads;
my $genome_path;
my $reads_selector;
my $input_read;
my $Read1fastqgz;
my $Read2fastqgz;
my $alignIntronMin;
my $alignIntronMax;   
my $outFilterMismatchNmax;
my $orientation;
my $refownfastaref;
my $refselector;
my $refowngtf;
my $compress;
my $cufflinks;
my $outputfile;
my $outputfileT;
my $outputlogSJ;
my $outputlogfinal;


Getopt::Long::Configure( 'no_ignorecase', 'bundling' );
GetOptions (
    'runThreadN=i' => \$Nthreads,
    'genomeDir=s' => \$genome_path,
    'refselector=s' => \$refselector,
    'refownfastaref=s' => \$refownfastaref,
    'refowngtf=s' => \$refowngtf,
    'compress=s' => \$compress,
    'cufflinks=s' => \$cufflinks,
    'readsselector=s'=> \$reads_selector,
    'readFilesIn1=s' => \$Read1fastqgz,
    'readFilesIn2=s' => \$Read2fastqgz,
    'readsinputread=s' => \$input_read,
    'alignIntronMin=i' => \$alignIntronMin,
    'alignIntronMax=i' => \$alignIntronMax,   
    'outFilterMismatchNmax=i' => \$outFilterMismatchNmax,
    'orientation=s' => \$orientation,
    'outputfile=s' => \$outputfile,
    'outputfileT=s' => \$outputfileT,
    'outputlogfinal=s' => \$outputlogfinal,
    'outputlogSJ=s' => \$outputlogSJ
) or die "Usage: Error in command line arguments\n";

my $cmd1 = ''; my $cmd2 ='';
my $cmd3 = ''; my $cmd4 ='';

#STAR --runThreadN 4 --runMode genomeGenerate --genomeDir /work/smaman/TP_RNAseq/INDEX/ --genomeFastaFiles ITAG2.3_genomic_Ch6.fasta --sjdbGTFfile ITAG_pre2.3_gene_models_Ch6.gtf --sjdbOverhang 100

#smaman@node001 /work/smaman/TP_RNAseq $ ls -ltrah INDEX
#-rw-r--r-- 1 smaman BIOINFO  331 17 juil. 11:55 genomeParameters.txt
#-rw-r--r-- 1 smaman BIOINFO 387K 17 juil. 11:55 exonGeTrInfo.tab
#-rw-r--r-- 1 smaman BIOINFO  53K 17 juil. 11:55 geneInfo.tab
#-rw-r--r-- 1 smaman BIOINFO 151K 17 juil. 11:55 transcriptInfo.tab
#-rw-r--r-- 1 smaman BIOINFO 171K 17 juil. 11:55 exonInfo.tab
#-rw-r--r-- 1 smaman BIOINFO 325K 17 juil. 11:55 sjdbList.fromGTF.out.tab
#-rw-r--r-- 1 smaman BIOINFO 272K 17 juil. 11:55 sjdbInfo.txt
#-rw-r--r-- 1 smaman BIOINFO 325K 17 juil. 11:55 sjdbList.out.tab
#-rw-r--r-- 1 smaman BIOINFO   11 17 juil. 11:55 chrName.txt
#-rw-r--r-- 1 smaman BIOINFO    9 17 juil. 11:55 chrLength.txt
#-rw-r--r-- 1 smaman BIOINFO   11 17 juil. 11:55 chrStart.txt
#-rw-r--r-- 1 smaman BIOINFO   20 17 juil. 11:55 chrNameLength.txt
#-rw-r--r-- 1 smaman BIOINFO  47M 17 juil. 11:55 Genome
#-rw-r--r-- 1 smaman BIOINFO 360M 17 juil. 11:55 SA
#-rw-r--r-- 1 smaman BIOINFO 1,5G 17 juil. 11:55 SAindex


#STAR --readFilesIn WTr1.fastq WTr2.fastq  --genomeDir /work/smaman/TP_RNAseq/INDEX/ --sjdbGTFfile ITAG_pre2.3_gene_models_Ch6.gtf   --outSAMtype BAM SortedByCoordinate --alignIntronMin 20 --alignIntronMax 1000000 --outFilterMismatchNmax 10 --outSAMtype BAM SortedByCoordinate --runThreadN 4 --outFileNamePrefix  galaxyName --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout  --quantMode TranscriptomeSAM 

#-rw-r--r--  1 smaman BIOINFO  45M 26 mars   2015 ITAG2.3_genomic_Ch6.fasta
#-rw-r--r--  1 smaman BIOINFO 1,6M 26 mars   2015 ITAG_pre2.3_gene_models_Ch6.gtf
#-rw-r--r--  1 smaman BIOINFO   29 26 mars   2015 ITAG2.3_genomic_Ch6.fasta.fai
#-rw-r--r--  1 smaman BIOINFO  614 17 juil. 10:20 WTr1.fastq
#-rw-r--r--  1 smaman BIOINFO  589 17 juil. 10:20 WTr2.fastq
#-rw-r--r--  1 smaman BIOINFO  14K 17 juil. 11:55 Log.out
#-rw-r--r--  1 smaman BIOINFO  35K 17 juil. 12:03 galaxyNameAligned.toTranscriptome.out.bam
#-rw-r--r--  1 smaman BIOINFO  637 17 juil. 12:03 galaxyNameAligned.sortedByCoord.out.bam +++++++++
#-rw-r--r--  1 smaman BIOINFO    0 17 juil. 12:03 galaxyNameSJ.out.tab            ++++++++++++++++
#-rw-r--r--  1 smaman BIOINFO  246 17 juil. 12:03 galaxyNameLog.progress.out
#-rw-r--r--  1 smaman BIOINFO 1,7K 17 juil. 12:03 galaxyNameLog.final.out   +++++++++++++++
#-rw-r--r--  1 smaman BIOINFO  16K 17 juil. 12:03 galaxyNameLog.out



#workspace
my $debug = 0; #Mode debug
if ($debug == 0)
	{
	print STDOUT "Debug mode OK \n";
	}
else	
	{
	$PATH = dirname($outputfile); 
	print STDOUT "No debug \n";
	}


#Récuperer le numero (unique) de l'output afin, si besoin, de créer un répertoire de travail unique dans /work/galaxy-dev/workspace
my ($nb) = ($outputfile=~/dataset_(\d+)\.\S+$/);

#Repertoire de sortie cree par le script, verif des droits d'ecriture sur ce repertoire de sortie
`cd $PATH/; mkdir $nb/; chmod -R 777 $nb/; cd $nb/;`;
my $dirresults= "$PATH/".$nb;

print STDOUT "Job working directory : $dirresults \n";


if ($refselector eq "ownfasta"){
        my $cmdSTARindex="(cd $dirresults/; mkdir INDEX/; chmod 777 INDEX/; $STAR --runThreadN $Nthreads --runMode genomeGenerate --genomeDir $dirresults/INDEX --genomeFastaFiles $refownfastaref --sjdbGTFfile $refowngtf --sjdbOverhang 100) >& ./out_Starindex.log 2>&1";
        system  $cmdSTARindex;
        #Info pour les biologistes
        print STDOUT "STAR Genome Generate : \n\n $cmdSTARindex \n\n ";
        $genome_path = "$dirresults/INDEX/";
}

my $addcuff;
if ($cufflinks eq "cuff"){
    $addcuff="--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --quantMode TranscriptomeSAM ";
}else{
    $addcuff="";
}


my $cat;
if ($reads_selector eq "single"){
                    
                my $in;    
                if ($compress eq "compress"){
                #Si besoin, recupération du fichier de configuration avec modification de l extension
                `ln -s $input_read $dirresults/input_read.fastq.gz;`;
                $in = "$dirresults/input_read.fastq.gz";
                $cat="--readFilesCommand zcat";
                }else
                {`ln -s $input_read $dirresults/input_read.fastq;`;
                $in = "$dirresults/input_read.fastq";
                $cat="";}

                if ($orientation eq "No"){
                    $cmd1 = "(cd $dirresults; $STAR  --runThreadN $Nthreads --genomeDir $genome_path --readFilesIn $in  --outSAMtype BAM SortedByCoordinate --alignIntronMin $alignIntronMin --alignIntronMax $alignIntronMax --outFilterMismatchNmax $outFilterMismatchNmax $cat  --outFileNamePrefix $nb $addcuff) >& ./out_Star.log 2>&1";
                    system $cmd1;
                    #Info pour les biologistes
                    print STDOUT "STAR command run on cluster without oriented reads : \n\n $cmd1 \n\n ";
                }
                else
                {
                    $cmd2 = "(cd $dirresults; $STAR --runThreadN $Nthreads --genomeDir $genome_path --readFilesIn $in  --outSAMtype BAM SortedByCoordinate --alignIntronMin $alignIntronMin --alignIntronMax $alignIntronMax --outFilterMismatchNmax $outFilterMismatchNmax $cat --outFileNamePrefix $nb $addcuff) >& ./out_Star.log 2>&1";
                     system  $cmd2;
                    #Info pour les biologistes
                    print STDOUT "STAR command run on cluster with oriented reads : \n\n $cmd2 \n\n 
                    Instead, you need to run Cufflinks with the library option --library-type options. For example, cufflinks <…> -library-type fr-firststrand should be used for the “standard” dUTP protocol. This option has to be used only for Cufflinks runs and not for STAR runs.\n\n";
                }
}else{
    
    
    my $in1;
    my $in2;
    if ($compress eq "compress"){
                #Si besoin, recupération du fichier de configuration avec modification de l extension
                `ln -s $Read1fastqgz $dirresults/Read1.fastq.gz; ln -s $Read2fastqgz $dirresults/Read2.fastq.gz;`;
                $in1="$dirresults/Read1.fastq.gz";
                $in2="$dirresults/Read2.fastq.gz";
                $cat="--readFilesCommand zcat";
                }else
                {`ln -s $Read1fastqgz $dirresults/Read1.fastq; ln -s $Read2fastqgz $dirresults/Read2.fastq;`;
                $in1="$dirresults/Read1.fastq";
                $in2="$dirresults/Read2.fastq";
                $cat="";}
                
                
   if ($orientation eq "No"){
                    $cmd3 = "(cd $dirresults; $STAR --runThreadN $Nthreads --genomeDir $genome_path --readFilesIn $in1 $in2  --outSAMtype BAM SortedByCoordinate --alignIntronMin $alignIntronMin --alignIntronMax $alignIntronMax --outFilterMismatchNmax $outFilterMismatchNmax  $cat --outFileNamePrefix $nb $addcuff) >& ./out_Star.log 2>&1";
                    system $cmd3;
                    #Info pour les biologistes
                    print STDOUT "STAR command run on cluster without oriented reads : \n\n $cmd3 \n\n ";
                }
                else
                {
                    $cmd4 = "(cd $dirresults; $STAR --runThreadN $Nthreads --genomeDir $genome_path --readFilesIn $in1 $in2  --outSAMtype BAM SortedByCoordinate --alignIntronMin $alignIntronMin --alignIntronMax $alignIntronMax --outFilterMismatchNmax $outFilterMismatchNmax $cat --outFileNamePrefix $nb $addcuff) >& ./out_Star.log 2>&1";
                    #Info pour les biologistes
                     system $cmd4;
                    print STDOUT "STAR command run on cluster with oriented reads : \n\n $cmd4 \n\n 
                    Instead, you need to run Cufflinks with the library option --library-type options. For example, cufflinks <…> -library-type fr-firststrand should be used for the “standard” dUTP protocol. This option has to be used only for Cufflinks runs and not for STAR runs.\n\n";
                }


}

#Si besoin :
#TEST 1 : command ligne on vm-galaxy
#TEST 2 perl Galaxy file : perl script.pl path/to/tests/files/used/for/galaxy/perl/script out1

#Recuperation des fichiers par Galaxy
#-rw-r--r--  1 smaman BIOINFO  35K 17 juil. 12:03 galaxyNameAligned.toTranscriptome.out.bam  +++++ 
#-rw-r--r--  1 smaman BIOINFO  637 17 juil. 12:03 galaxyNameAligned.sortedByCoord.out.bam +++++++++
#-rw-r--r--  1 smaman BIOINFO    0 17 juil. 12:03 galaxyNameSJ.out.tab            ++++++++++++++++
#-rw-r--r--  1 smaman BIOINFO 1,7K 17 juil. 12:03 galaxyNameLog.final.out   +++++++++++++++
my $bam = glob("$dirresults/*$nb*Aligned.sortedByCoord.out.bam");
if (! -e $bam){print STDERR "Aligned.sortedByCoord.out.bam file not found. \n";}else{`cp -a $bam $outputfile`;}
my $bamT = glob("$dirresults/*$nb*Aligned.toTranscriptome.out.bam");
if (! -e $bamT){print STDERR "Aligned.toTranscriptome.out.bam file not found. \n";}else{`cp -a $bamT $outputfileT`;}
my $logSJ = glob("$dirresults/$nb*SJ.out.tab");
if (! -e $logSJ){print STDERR "SJ.out.tab log file not found. \n";}else{`cp -a $logSJ $outputlogSJ`;}
my $logfinal = glob("$dirresults/$nb*Log.final.out");
if (! -e $logfinal){print STDERR "Log.final.out log file not found. \n";}else{`cp -a $logfinal $outputlogfinal`;}