--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commet.py	Fri Jun 05 11:41:26 2015 -0400
@@ -0,0 +1,129 @@
+#!/usr/bin/env python
+import sys, tempfile, subprocess, glob
+import os, re, shutil, optparse
+import zipfile, tarfile, gzip
+from os.path import basename
+
+"""
+WARNING :
+
+commet.py needs commet_exe binaries in your $PATH
+
+commet is available after compiling sources :
+
+http://github.com/pierrepeterlongo/commet
+
+or with the galaxy_commet package in the GenOuest toolshed (coming soon)
+
+NOTE : 
+
+please add the line #!/usr/bin/env python in top of the Commet.py file if you've a bash error.
+
+
+"""
+
+def __main__():
+
+	# arguments recuperation
+        parser = optparse.OptionParser()
+        parser.add_option("--input", dest="input")
+        parser.add_option("-k", dest="kmer")
+        parser.add_option("-t", dest="minsharedkmer")
+        parser.add_option("-l", dest="minlengthread")
+        parser.add_option("-n", dest="maxn")
+        parser.add_option("-e", dest="minshannonindex")
+        parser.add_option("-m", dest="maxreads")
+
+        parser.add_option("--output")
+        parser.add_option("--output_vectors")
+        parser.add_option("--output_dendro")
+        parser.add_option("--output_logs")
+        parser.add_option("--output_matrix")
+        parser.add_option("--output_heatmap1")
+        parser.add_option("--output_heatmap2")
+        parser.add_option("--output_heatmap3")
+
+        (options, args) = parser.parse_args()
+
+
+	# copy R script into the current dir
+	shutil.copy(os.environ['RSCRIPTS']+"/heatmap.r", os.getcwd())
+        shutil.copy(os.environ['RSCRIPTS']+"/dendro.R", os.getcwd())
+
+	# remove the first line of the input file
+	commet_file = open(options.input, "r")
+	commet_file_clean = open("commet_clean_file", "w")
+
+	# delete the first line
+	commet_file.readline()
+	for line in commet_file:
+		commet_file_clean.write(line)
+
+	# close files
+	commet_file.close()
+	commet_file_clean.close()
+
+	# edit the command line
+	cmd_line=[]
+	cmd_line.append("Commet.py")
+	cmd_line.extend(["commet_clean_file","-b",os.environ['BINARIES'],"-k",options.kmer,"-t",options.minsharedkmer,"-l",options.minlengthread,"-e",options.minshannonindex])
+
+	# add options
+	if options.maxn:
+		
+		#cmd_line += ' -n '+options.maxn+' -m '+options.maxreads+' > '+options.output+' 2>>'+options.output
+		cmd_line.extend(["-n",options.maxn,"-m",options.maxreads])
+	#else:
+		#cmd_line += ' > '+options.output+' 2>>'+options.output
+
+	# execute job
+	p=subprocess.Popen(cmd_line,
+                   stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+
+	stdoutput, stderror = p.communicate()
+
+	# log file
+        logfile=open(options.output, "w")
+	logfile.write("[COMMAND LINE]"+' '.join(cmd_line)+"\n\n")
+	logfile.write(str(stdoutput))
+	logfile.write(str(stderror))
+	logfile.close()
+
+	# copy .bv files inside a .bv archive
+	tmp_output_dir=os.getcwd()+"/output_commet/"
+        os.chdir(tmp_output_dir)
+
+	# create zip outputs
+        mybvzipfile=zipfile.ZipFile(tmp_output_dir+'bv.zip.temp', 'w')
+        mylogzipfile=zipfile.ZipFile(tmp_output_dir+'log.zip.temp', 'w')
+        mymatrixzipfile=zipfile.ZipFile(tmp_output_dir+'matrix.zip.temp', 'w')
+
+	# write files into the specific archive
+        list_files = glob.glob(tmp_output_dir+'/*')
+        for i in list_files:
+
+		if re.search("\.bv$", i):
+			mybvzipfile.write(os.path.basename(i))
+		if re.search("\.log$", i):
+                        mylogzipfile.write(os.path.basename(i))
+		if re.search(".csv$", i):
+                        mymatrixzipfile.write(os.path.basename(i))
+
+	# close zip files
+	mybvzipfile.close()
+	mylogzipfile.close()
+        mymatrixzipfile.close()
+
+	# return the archives
+	shutil.move(tmp_output_dir+'bv.zip.temp', options.output_vectors)
+	shutil.move(tmp_output_dir+'log.zip.temp', options.output_logs)
+        shutil.move(tmp_output_dir+'matrix.zip.temp', options.output_matrix)
+
+	# outputs
+        shutil.move(tmp_output_dir+'dendrogram_normalized.png', options.output_dendro)
+	shutil.move(tmp_output_dir+'heatmap_normalized.png', options.output_heatmap1)
+	shutil.move(tmp_output_dir+'heatmap_percentage.png', options.output_heatmap2)
+	shutil.move(tmp_output_dir+'heatmap_plain.png', options.output_heatmap3)
+
+if __name__ == "__main__": __main__()
+