Python Popen.start方法代码示例

# 需要导入模块: from subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import start [as 别名]
def main():
  parser = argparse.ArgumentParser(description="Split aligned reads into chromosomes",formatter_class=argparse.ArgumentDefaultsHelpFormatter)
  parser.add_argument('input',help="sorted samtools indexed BAM file")
  parser.add_argument('-o','--output',help="output directory")
  args = parser.parse_args()
  m = re.search('([^\/]+)\.bam$',args.input)
  if not m: 
    sys.stderr.write("bam file must end in .bam")
    sys.exit()
  basename = m.group(1)
  args.output = args.output.rstrip('/')
  if not os.path.exists(args.output):
    os.makedirs(args.output)
  cmd = "samtools view -H "+args.input
  p = Popen(cmd.split(),stdout=PIPE)
  chrs = []
  for line in p.stdout:
    m = re.match('@SQ\tSN:(\S+)',line)
    if not m: continue
    chrs.append(m.group(1))
  p.communicate()
  ps = []
  for chr in chrs:
    ps.append(Process(target=do_chr,args=(chr,args,basename,)))
  ps.append(Process(target=do_un,args=(args,basename,)))
  for p in ps: p.start()
  for p in ps: p.join()

# 需要导入模块: from subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import start [as 别名]

#.........这里部分代码省略.........
        The actual state should not be updated at the end,
        as this method could be
        called multiple times for the same solution step
        until the global convergence
        is reached. When global convergence is reached,
        finishStep is called and then
        the actual state has to be updated.
        Solution can be split into individual stages
        identified by optional stageID parameter.
        In between the stages the additional data exchange can be performed.
        See also wait and isSolved services.

        :param TimeStep tstep: Solution step
        :param int stageID: optional argument identifying
               solution stage (default 0)
        :param bool runInBackground: optional argument, defualt False.
               If True, the solution will run in background (in separate thread
               or remotely).

        """
        # Check that old simulation is not running:
        if not self.isSolved():
            return

        # Set current tstep
        self._curTStep = tstep

      
        # This thread will callback when tracer has ended.
        self.postThread = threading.Thread(target=self._runCallback,
                                           args=(self.tracerProcess,
                                                 self._tracerProcessEnded))
        # Post processing thread will wait for the tracer to finnish
        self.postThread.start()

        # Wait for process if applicaple
        if not runInBackground:
            self.wait()

    def wait(self):
        """
        Wait until solve is completed when executed in background.
        """
        print("Waiting...")
        self.tracerProcess.wait()
        print("Post processing...")
        self.postThread.join()
        print("Post processing done!")

    def isSolved(self):
        """
        :return: Returns true or false depending whether solve has completed
                 when executed in background.
        :rtype: bool
        """
        if self.tracerProcess.poll() is not None:
            return True
        if self.postThread.poll() is not None:
            return True
        return False


    def getCriticalTimeStep(self):
        """
        :return: Returns the actual (related to current state) critical time
        step increment

# 需要导入模块: from subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import start [as 别名]

#.........这里部分代码省略.........
        # Check that old simulation is not running:
        if not self.isSolved():
            return

        # Check params and fields
        initConf.checkRequiredFields(self.fields, FieldID)
        initConf.checkRequiredParameters(self.properties, PropertyID)
        initConf.checkRequiredFunctions(self.functions, fID=FunctionID)

        # Set current tstep and copy previous results as starting values
        self._curTStep = tstep
        self._copyPreviousSolution()

        # Write out JSON file.
        self._writeInputJSON(tstep)

        # Get mie data from other app
        self._getMieData(tstep)

        # Start thread to start calculation
        self.tracerProcess = Popen(  # ["ping", "127.0.0.1",  "-n",
            # "3", "-w", "10"],
            # self.tracerProcess = Popen(["tracer",
            # "DefaultLED.json"],
            ["tracer-no-ray-save", "input.json"],
            stdout=PIPE,
            stderr=PIPE)

        # This thread will callback when tracer has ended.
        self.postThread = threading.Thread(target=self._runCallback,
                                           args=(self.tracerProcess,
                                                 self._tracerProcessEnded))
        # Post processing thread will wait for the tracer to finnish
        logger.info('Ray tracing starting...')
        self.postThread.start()

        # Wait for process if applicaple
        if not runInBackground:
            self.wait()

    def wait(self):
        """
        Wait until solve is completed when executed in background.
        """
        logger.debug("Tracing...")
        self.tracerProcess.wait()
        logger.debug("Post processing...")
        self.postThread.join()
        logger.debug("Post processing done!")

    def isSolved(self):
        """
        :return: Returns true or false depending whether solve has completed
                 when executed in background.
        :rtype: bool
        """
        if self.tracerProcess.poll() is not None:
            return True
        if self.postThread.poll() is not None:
            return True
        return False

    def getCriticalTimeStep(self):
        """
        :return: Returns the actual (related to current state) critical time
        step increment

# 需要导入模块: from subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import start [as 别名]
    fnull = open(os.devnull,'w')
    p = call(cmd,stdout=fnull,shell=True)
    fnull.close()
    print "** Generating new *.xml files **"
    writeToLog(logfile,"** Generating new *.xml files **")
    i = 0

    # Loop through all inpaths and outfiles
    while i <= (len(outfiles)-threadCount):
        # Case where full threads are used
        threads = threadCount
        # Create queue and pool variables
        queue0 = manager0.Queue() ; pool = []
        for n in range(threads):
            p =  Process(target=xmlWrite,args=(outfiles_paths[i+n],outfiles[i+n],host_path,cdat_path,start_time,queue0))
            p.start() ; pool.append(p)

        # Wait for processes to terminate
        for p in pool:
            p.join()

        # Get data back from queue object
        inpaths = [] ; outfileNames = [] ; fileZeros = [] ; fileWarnings = [] ; fileNoReads = [] ; fileNoWrites = [] ; fileNones = [] ; errorCodes = [] ; time_since_starts = []
        while not queue0.empty():
            [inpath,outfileName,fileZero,fileWarning,fileNoRead,fileNoWrite,fileNone,errorCode,time_since_start] = queue0.get_nowait()
            inpaths.append(inpath)
            outfileNames.append(outfileName)
            fileZeros.append(fileZero)
            fileWarnings.append(fileWarning)
            fileNoReads.append(fileNoRead)
            fileNoWrites.append(fileNoWrite)