diff TakeABreak_wrapper.py @ 0:dbd6e370c891

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TakeABreak_wrapper.py	Fri Jun 05 11:40:02 2015 -0400
@@ -0,0 +1,83 @@
+import sys, tempfile, subprocess, glob
+import os, re, shutil
+import optparse
+from os.path import basename
+
+"""
+
+Created by Cyril Monjeaud
[e-mail]
+
+WARNING :
+
+TakeABreak_wrapper.py needs:
+
+- dbgh5 & TakeABreak binaries in your $PATH
+
+All these files are available after compiling the sources of TakeABreak :
+
+http://colibread.inria.fr/files/2014/01/TakeABreak-1.1.0-Source.tar_.gz
+
+or with the package_takeabreak dependency in the toolshed
+
+"""
+
+def __main__():
+
+	# create a special dir inside job working dir
+        tmp_dir = tempfile.mkdtemp()
+        os.chdir(tmp_dir)
+
+        # retrieve arguments
+        parser = optparse.OptionParser()
+        parser.add_option("-i", dest="reads_files")
+        parser.add_option("-k", dest="kmer")
+        parser.add_option("-S", dest="kmersolid")
+
+        parser.add_option("-g", dest="graph_file")
+        parser.add_option("-c", dest="complexity")
+        parser.add_option("-m", dest="maxsimprct")
+        parser.add_option("-r", dest="optimization")
+
+        parser.add_option("--output_graph")
+        parser.add_option("--output_fasta")
+        parser.add_option("--output_log")
+
+        (options, args) = parser.parse_args()
+	
+	cmd_line=[]
+	if options.reads_files:
+		# start the command line
+		cmd_line.append("TakeABreak")
+		cmd_line.extend(["-in",options.reads_files,"-kmer-size",options.kmer,"-abundance",options.kmersolid])
+	else:
+		# start the command line
+		os.symlink(options.graph_file, "graph.h5")
+		cmd_line.append("TakeABreak")
+		cmd_line.extend(["-graph", "graph.h5"])
+
+	cmd_line.extend(["-out","galaxy","-lct",options.complexity,"-max-sim",options.maxsimprct,"-repeat",options.optimization])
+
+	# execute command line 
+	p=subprocess.Popen(cmd_line,
+                   stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+
+	stdoutput, stderror = p.communicate()
+
+        # log file
+        logfile=open(options.output_log, "w")
+	logfile.write("[COMMAND LINE]"+' '.join(cmd_line)+"\n\n")
+        logfile.write(stdoutput)
+	logfile.write(stderror)
+	logfile.close()
+	
+	if options.reads_files:
+
+                # create output h5
+		shutil.copy("galaxy.h5", options.output_graph)
+
+        # create output fasta
+	shutil.copy("galaxy.fasta", options.output_fasta)
+
+if __name__ == "__main__": __main__()
+