diff VCFStorage_wrapper.py @ 0:3552a8d9f51c draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/VCFStorage_wrapper.py	Tue Nov 10 08:30:56 2015 -0500
@@ -0,0 +1,96 @@
+#!/usr/bin/env python
+
+
+import subprocess, tempfile, sys, os, glob, shutil, time, random
+from optparse import OptionParser
+from optparse import Option, OptionValueError
+
+class VCFStorageWrapper(object):
+
+	def __init__(self):
+		self._options = None
+		
+		
+	def stop_err(self, msg ):
+		sys.stderr.write( "%s\n" % msg )
+		sys.exit()
+		
+		
+	def setAttributesFromCmdLine(self):
+		description = "VCFStorage_wrapper"
+		description += "\nWrapper for VCFStorage\n VCFStorage "
+		description += "VCFStorage stores info from variant calling into a table. It will create a tabulate file with the different infos\n"
+		description += "example : VCFStorage -f fasta.fa -l genomelist.list -w workdir -o output.tab \n"
+		parser = OptionParser(description = description, version = "0.1")
+		parser.add_option("-f", "--fasta",            dest = "fastaFile",      action = "store",     type = "string", help = "Input fasta file name [compulsory] [format: Fasta]",                default = "")
+		parser.add_option("-l", "--genomeNameList",   dest = "genomeNameList", action = "append",    type = "string", help = "Input list of genome name ")
+		parser.add_option("-L", "--genomeFileList",   dest = "genomeFileList", action = "append",    type = "string", help = "Input list of genome VCF file ")
+		parser.add_option("-w", "--workDir",          dest = "workDir",        action = "store",     type = "string", help = "name of the workingDirectory",                                      default = "")
+		parser.add_option("-o", "--out",              dest = "outFile",        action = "store",     type = "string", help = "Output file name [compulsory] [format: tab]",                       default = "")
+		options = parser.parse_args()[0]
+		self._setAttributesFromOptions(options)
+
+
+	def _setAttributesFromOptions(self, options):
+		self._options = options
+
+	def run(self):
+		self.createGenomeList()
+		cmd = self.createCmdLine()
+		self.launchCmdLine(cmd)
+		
+	def createGenomeList(self):
+		self.genomelistFile = "%s.genomeListFile" % self._options.outFile
+		lGenomeName = self._options.genomeNameList
+		lGenomeVCF = self._options.genomeFileList
+		output = open(self.genomelistFile, "w")
+		for i,genomeName in enumerate(lGenomeName) :
+			output.write("%s\t%s\n" % (lGenomeName[i],lGenomeVCF[i]))
+		output.close()
+		
+	def createCmdLine(self):
+		workdir = "VCFStorage_%s_%d" % (time.strftime("%d%H%M%S"), random.randint(0, 10000))
+		prg = "VCFStorage.py"
+		args = ""
+		args += "-f %s" % self._options.fastaFile
+		args += " "
+		args += "-o %s" % self._options.outFile
+		args += " "
+		args += "-l %s" % self.genomelistFile
+		args += " "
+		args += "-w %s" % workdir
+		cmd = "%s %s" %(prg, args)
+		
+		print cmd
+		return cmd
+		
+	def launchCmdLine(self, cmd):
+		try:
+			tmp_err = tempfile.NamedTemporaryFile().name
+			tmp_stderr = open( tmp_err, 'wb' )
+			proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr )
+			returncode = proc.wait()
+			tmp_stderr.close()
+			# get stderr, allowing for case where it's very large
+			tmp_stderr = open( tmp_err, 'rb' )
+			stderr = ''
+			buffsize = 1048576
+			try:
+				while True:
+					stderr += tmp_stderr.read( buffsize )
+					if not stderr or len( stderr ) % buffsize != 0:
+						break
+			except OverflowError:
+				pass
+			tmp_stderr.close()
+			if stderr:
+				raise Exception, stderr
+		except Exception, e:
+			os.remove(self.genomelistFile)
+			self.stop_err( 'Error in VCFStorage:\n' + str( e ) ) 
+		os.remove(self.genomelistFile)
+
+if __name__ == "__main__":
+	iWrapper = VCFStorageWrapper()
+	iWrapper.setAttributesFromCmdLine()
+	iWrapper.run()