diff mapsembler2.py @ 0:f905f982ee3d

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mapsembler2.py	Fri Jun 05 11:40:49 2015 -0400
@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+import sys, subprocess, glob
+import os, re, shutil, optparse
+from os.path import basename
+
+"""
+WARNING :
+
+Mapsembler2.py needs mapsembler2_exe binaries in your $PATH
+
+Mapsember2 is available after compiling sources :
+
+http://www.irisa.fr/symbiose/people/ppeterlongo/mapsembler2_2.2.3.zip
+
+or with the galaxy_mapsembler2 package in the GenOuest toolshed
+
+
+"""
+
+def __main__():
+
+	# arguments recuperation
+        parser = optparse.OptionParser()
+        parser.add_option("-s", dest="input_starters")
+        parser.add_option("-r", dest="input_files")
+        parser.add_option("-t", dest="output_extension")
+        parser.add_option("-k", dest="kmer")
+        parser.add_option("-c", dest="coverage")
+        parser.add_option("-d", dest="substitutions")
+        parser.add_option("-g", dest="genome_size")
+        parser.add_option("-f", dest="process_search")
+        parser.add_option("-x", dest="max_length")
+        parser.add_option("-y", dest="max_depth")
+        parser.add_option("--output")
+        parser.add_option("-i", dest="index_files")
+
+        (options, args) = parser.parse_args()
+
+	# import tools
+	os.symlink(os.environ['TOOLS'], os.getcwd()+'/tools')
+
+	# execute mapsembler
+	cmd_line=[]
+	cmd_line.append("run_mapsembler2_pipeline.sh")
+
+	# change starter extension
+	cmd_line.extend(["-s", options.input_starters])
+
+	#inputs
+	cmd_line.append("-r")
+
+	#cmd_line.append(inputs)
+	cmd_line.append(' '.join(options.input_files.split(",")))
+
+	# add parameters into the command line
+	cmd_line.extend(["-t", options.output_extension, "-k", options.kmer, "-c", options.coverage, "-d", options.substitutions, "-g", options.genome_size, "-f", options.process_search, "-x", options.max_length, "-y", options.max_depth])
+	
+	# open the output log file
+        log = open(options.output, "w")
+	log.write("[COMMAND LINE] "+' '.join(cmd_line))
+
+	process=subprocess.Popen(cmd_line,
+                   stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+
+        stdoutput, stderror = process.communicate()
+	
+	# results recuperation
+	log.write(stdoutput)
+	log.write(stderror)
+
+	# close log file
+	log.close()
+	
+	# move results files inside the job_outputs dir
+	os.mkdir("job_outputs")
+	result_files = glob.glob("res_*")
+	for file in result_files:
+		shutil.move(file, "job_outputs/")
+
+
+	# move index files
+	if options.index_files == "true":
+	        index_files = glob.glob("index_*")
+		for index in index_files:
+			shutil.move(index, "job_outputs/")
+
+	# move json result into gjson
+        json_files = glob.glob("job_outputs/*.json")
+        for json in json_files:
+		shutil.move(json, json.replace(".json", ".gjson"))
+
+
+if __name__ == "__main__": __main__()
+