--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bbric_disco.py	Fri Jun 05 11:40:18 2015 -0400
@@ -0,0 +1,126 @@
+import sys, tempfile, subprocess, glob
+import os, re, shutil, stat
+import optparse
+from os.path import basename
+
+"""
+
+Created by Cyril Monjeaud
+Cyril.Monjeaud@irisa.fr
+Modified by Fabrice Legeai
+fabrice.legeai@rennes.inra.fr
+
+Last modifications : 04/21/2015
+
+WARNING :
+
+discoSNP++.py needs:
+
+- run_discoSnp++.sh
+- discoSNP++_to_genotypes.py
+- the build repository next to the scripts
+
+All these files are available after compiling the sources of discoSNP :
+
+https://colibread.inria.fr/files/2013/10/DiscoSNPpp-2.0.6-Source.zip
+
+or with the package_discoSnp_plus_plus package in the toolshed
+
+"""
+
+
+def __main__():
+
+	# store inputs in an array
+	parser = optparse.OptionParser()
+	parser.add_option("-r", dest="data_files")
+	parser.add_option("-b", dest="branching_bubbles")
+	parser.add_option("-D", dest="deletions")
+	parser.add_option("-P", dest="min_snps")
+	parser.add_option("-l", action="store_true", dest="low_complexity")
+	parser.add_option("-k", dest="kmer")
+	parser.add_option("-t", action="store_true", dest="left_right_unitigs")
+	parser.add_option("-T", action="store_true", dest="left_right_contigs")
+	parser.add_option("-c", dest="coverage")
+        parser.add_option("-C", dest="maxcoverage")
+	parser.add_option("-d", dest="error_threshold")
+	parser.add_option("-n", action="store_true", dest="genotypes")
+	parser.add_option("-G", dest="reference")
+        parser.add_option("-M", dest="mapping_error")
+
+	(options, args) = parser.parse_args()
+
+        # create the working dir inside job_working_dir
+        output_dir = os.mkdir("job_outputs")
+
+	cmd_line=[]
+	cmd_line.append("/bin/bash")
+	#cmd_line.append("/home/genouest/inrarennes/flegeai/local/DiscoSNP/DiscoSNP++-2.1.4-Source/run_discoSnp++.sh")
+	cmd_line.append("run_discoSnp++.sh")
+	#cmd_line.append("-B /local/bwa/bwa-0.7.10/")
+
+	# transform .dat into .fasta or .fastq for kissreads2
+	link_files=[]
+	f = open(options.data_files, 'r')
+	files = f.readlines()
+	for file in files:
+		file=file.strip()
+		if re.search("^$",file): continue
+		tagfile=[]
+		tagfile=re.split('::', file)	
+		number = int(tagfile[0])+1
+		if re.search("^>.*", open(tagfile[1]).readline()):
+                        link_file = 'input'+str(number)+'.fasta'
+                else:
+                        link_file = 'input'+str(number)+'.fastq'
+
+                os.symlink(tagfile[1], link_file)
+                link_files.append(link_file)
+
+
+	# edit the command line
+	cmd_line.extend(["-r",' '.join(link_files),"-b",options.branching_bubbles,"-D",options.deletions,"-P",options.min_snps,"-k",options.kmer,"-c",options.coverage,"-C",options.maxcoverage,"-d",options.error_threshold])
+	if options.low_complexity:
+		cmd_line.append("-l")
+	if options.left_right_unitigs:
+		cmd_line.append("-t")
+	if options.left_right_contigs:
+                cmd_line.append("-T")
+	if options.genotypes:
+		cmd_line.append("-n")
+
+	# genotype part
+	if options.reference:
+		cmd_line.extend(["-G", options.reference])
+		cmd_line.extend(["-M", options.mapping_error])
+
+	cmd_line.extend(["-p","job_outputs/galaxy"])
+
+	# execute job
+	p=subprocess.Popen(cmd_line,
+                   stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+
+	stdoutput, stderror = p.communicate()
+
+	# report file
+        logfile=open("report.txt", "w")
+	logfile.write("[COMMAND LINE]"+' '.join(cmd_line)+"\n\n")
+	logfile.write(stdoutput)
+
+	# print stderror because it's informations
+        logfile.write(stderror)
+
+	# close logfile
+	logfile.close()
+
+	# change .fa extension to .fasta for a correct print inside Galaxy
+        fafiles = glob.glob("job_outputs/*_coherent.fa")
+	for fafile in fafiles:
+        	shutil.move(fafile, "coherent.fasta")
+        vcffiles = glob.glob("job_outputs/*_coherent.vcf")
+	for vcffile in vcffiles:
+        	shutil.move(vcffile, "coherent.vcf")
+
+
+if __name__ == "__main__": __main__()
+