Python Popen.join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 join [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 join [as 别名]
def main():
  parser = argparse.ArgumentParser(description="",formatter_class=argparse.ArgumentDefaultsHelpFormatter)
  parser.add_argument('input',help="Sorted bam (preferrably indexed) Use - for STDIN sam. If streaming in be sure to remove unmapped reads")
  parser.add_argument('--threads',type=int,default=1,help="use multiple threads the bam has been indexed.  Order is not preserved.")
  args = parser.parse_args()


  single_thread = True
  if args.threads == 1: single_thread = True
  elif args.input != '-':
    if os.path.isfile(args.input+'.bai'): single_thread = False
    else: 
      single_thread = True
      sys.stderr.write("Warning doing single thread because lacking index\n")

  chrs = None
  if args.input != '-':
    chrs = set()
    cmd = 'samtools view -H '+args.input
    p = Popen(cmd.split(),stdout=PIPE)
    for line in p.stdout:
      m = re.match('@SQ\s+SN:(\S+)\s+LN:\d+',line)
      if m: chrs.add(m.group(1))
    p.communicate()
  #easy case of single thread
  if single_thread:
    if args.input == '-':
      dostream(sys.stdin)
    else:
      cmd = 'samtools view -F 4 -h '+args.input
      p = Popen(cmd.split(),stdout=PIPE)
      dostream(p.stdout)
      p.communicate()
  else:
    p = Pool(processes=args.threads)
    for chr in sorted(chrs):
      p.apply_async(dofilestream,args=(args.input,chr),callback=printres)
    p.close()
    p.join()

# 需要导入模块: from subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import join [as 别名]
def main():
  parser = argparse.ArgumentParser(description="Takes a BAM file preferably one already filtered to be uniquely mapped reads.")
  parser.add_argument('input_fasta',help="FASTAFILE indexed")
  parser.add_argument('input_sorted_bam',help="BAMFILE sorted indexed")
  parser.add_argument('--threads',type=int,default=multiprocessing.cpu_count(),help="Number of threads defautl cpu_count")
  parser.add_argument('--include_multiply_mapped_reads',action='store_true',help="Include multiply mapped reads that are excluded by default.  Note that this feature is not complete as it is with the 256 sam filter.  it will only remove secondary alignments while still leaving the multiply mapped primary alignments.  To only use uniquely mapped reads you need to pre-filter on unique and start from that indexed bam.")
  parser.add_argument('--include_indels',action='store_true',help="By default only SNPs and only loci with multiple genotypes are output.  This will output indels.")
  parser.add_argument('--consensus',action='store_true',help="Use the original caller")
  args = parser.parse_args()
  #read the sam header  
  p = Popen(('samtools view -H '+args.input_sorted_bam).split(),stdout=PIPE)
  chromlens = {}
  for line in p.stdout:
    m = re.match('@SQ\s+SN:(\S+)\s+LN:(\d+)',line.rstrip())
    if not m: continue
    chromlens[m.group(1)] = int(m.group(2))
  #Lets break these up now
  z = 0
  itersize = 10000000
  for chrom in chromlens:
    for i in range(1,chromlens[chrom],itersize):
      z+=1
  global gtotal
  gtotal = z
  if args.threads > 1:
    p = multiprocessing.Pool(processes=args.threads)
  for chrom in chromlens:
    for i in range(1,chromlens[chrom],itersize):
      rstart = i
      rend = itersize+i-1
      if rend > chromlens[chrom]: rend = chromlens[chrom]
      if args.threads <= 1:
        v = get_region_vcf(args,chrom,rstart,rend)
        do_output(v)
      else:
        p.apply_async(get_region_vcf,args=(args,chrom,rstart,rend),callback=do_output)
  if args.threads > 1:
    p.close()
    p.join()

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

#.........这里部分代码省略.........
        :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
        :rtype: float
        """
        # TODO: Check
        return np.Infinity  # Tracer does not have any time dependence...


    def getAPIVersion(self):
        """
        :return: Returns the supported API version
        :rtype: str, int
        """
        # TODO: API version support?? How
        return('1.0', 1)

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

#.........这里部分代码省略.........
        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
        :rtype: float
        """
        # TODO: Check
        return np.Infinity  # Tracer does not have any time dependence...

    def getAPIVersion(self):
        """
        :return: Returns the supported API version
        :rtype: str, int
        """
        # TODO: API version support?? How
        return('1.0', 1)

    def getApplicationSignature(self):

# 需要导入模块: from subprocess import Popen [as 别名]
# 或者: from subprocess.Popen import join [as 别名]
    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)
            fileNones.append(fileNone)
            errorCodes.append(errorCode)
            time_since_starts.append(time_since_start)