本文整理汇总了Python中subprocess32.call方法的典型用法代码示例。如果您正苦于以下问题:Python subprocess32.call方法的具体用法?Python subprocess32.call怎么用?Python subprocess32.call使用的例子?那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类subprocess32
的用法示例。
在下文中一共展示了subprocess32.call方法的13个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: fastq_bwa_mem_piped
# 需要导入模块: import subprocess32 [as 别名]
# 或者: from subprocess32 import call [as 别名]
def fastq_bwa_mem_piped(fastqs,i,j,t,rg,out_dir,ref_path):
output = ''
bam = out_dir+'/'+fastqs[0].rsplit('/')[-1].rsplit('.fq')[0].rsplit('_')[0]+'.%s.bam'%j
piped_mem = [bwa_mem,'-M','-t %s'%t,'-R',r"'%s'"%rg,ref_path,
'<(%s -f %s -i %s -j %s)'%(route,fastqs[0],i,j),
'<(%s -f %s -i %s -j %s)'%(route,fastqs[1],i,j),
'|',samtools_view,'-Sb','-','-@ %s'%t,
'|',sambamba_sort,'-t %s'%t,'--tmpdir=%s/temp'%out_dir,'-o',bam,'/dev/stdin'] #-@ for threads here
try:#bwa mem call here-------------------------------------------
output += subprocess.check_output(' '.join(piped_mem),
stderr=subprocess.STDOUT,
executable='/bin/bash',
shell=True)
output += subprocess.check_output(['rm','-rf','%s/temp'%out_dir])
except Exception as E:
output += str(E) #error on the call-------------------------
return bam #list of bam files to merge into next step
#|| by number of fastq files presented
示例2: call
# 需要导入模块: import subprocess32 [as 别名]
# 或者: from subprocess32 import call [as 别名]
def call(cmdline, environ=(), **kwargs):
"""Runs command wrapping subprocess.call.
:param cmdline:
Command to run
:type cmdline:
``list``
:param environ:
*optional* Environ variable to set prior to running the command
:type environ:
``dict``
"""
_LOGGER.debug('run: %r', cmdline)
args = _alias_command(cmdline)
# Setup a copy of the environ with the provided overrides
cmd_environ = dict(os.environ.items())
cmd_environ.update(environ)
rc = subprocess.call(args, close_fds=_CLOSE_FDS, env=cmd_environ, **kwargs)
_LOGGER.debug('Finished, rc: %d', rc)
return rc
示例3: run_cmd
# 需要导入模块: import subprocess32 [as 别名]
# 或者: from subprocess32 import call [as 别名]
def run_cmd(cmd):
out = []
fh = NamedTemporaryFile(delete=False)
es = subprocess.call(cmd, stdin=None,
stdout=fh, stderr=subprocess.STDOUT, shell=True)
fh.close()
with open(fh.name, 'r') as f:
for line in f:
out.append(line.rstrip('\n'))
os.unlink(fh.name)
if (es != 0):
print "[-] Non-zero exit status '%d' for CMD: '%s'" % (es, cmd)
for line in out:
print line
return es, out
示例4: grabLicence
# 需要导入模块: import subprocess32 [as 别名]
# 或者: from subprocess32 import call [as 别名]
def grabLicence(self):
"""
Returns True if a CPLEX licence can be obtained.
The licence is kept until releaseLicence() is called.
"""
status = ctypes.c_int()
# If the config file allows to do so (non null params), try to
# grab a runtime license.
if ilm_cplex_license and ilm_cplex_license_signature:
runtime_status = CPLEX_DLL.lib.CPXsetstaringsol(
ilm_cplex_license,
ilm_cplex_license_signature)
# if runtime_status is not zero, running with a runtime
# license will fail. However, no error is thrown (yet)
# because the second call might still succeed if the user
# has another license. Let us forgive bad user
# configuration:
if not (runtime_status == 0) and self.msg:
print(
"CPLEX library failed to load the runtime license" +
"the call returned status=%s" % str(runtime_status) +
"Please check the pulp config file.")
self.env = CPLEX_DLL.lib.CPXopenCPLEX(ctypes.byref(status))
self.hprob = None
if not(status.value == 0):
raise PulpSolverError("CPLEX library failed on " +
"CPXopenCPLEX status=" + str(status))
示例5: up_node1
# 需要导入模块: import subprocess32 [as 别名]
# 或者: from subprocess32 import call [as 别名]
def up_node1():
subproc.check_call(['vagrant', 'destroy', '-f', 'node1'])
subproc.check_call(['vagrant', 'up', 'node1', '--no-provision'])
yield "node1 is ready"
print("Destroying node1...")
subproc.call(['vagrant', 'destroy', '-f', 'node1'])
print("Node1 is destroyed.")
示例6: up_node2
# 需要导入模块: import subprocess32 [as 别名]
# 或者: from subprocess32 import call [as 别名]
def up_node2():
subproc.check_call(['vagrant', 'destroy', '-f', 'node2'])
subproc.check_call(['vagrant', 'up', 'node2'])
yield "node2 is ready"
print("Destroying node2...")
subproc.call(['vagrant', 'destroy', '-f', 'node2'])
print("Node2 is destroyed.")
示例7: up_node3
# 需要导入模块: import subprocess32 [as 别名]
# 或者: from subprocess32 import call [as 别名]
def up_node3():
subproc.check_call(['vagrant', 'destroy', '-f', 'node3'])
subproc.check_call(['vagrant', 'up', 'node3'])
yield "node3 is ready"
print("Destroying node3...")
subproc.call(['vagrant', 'destroy', '-f', 'node3'])
print("Node3 is destroyed.")
示例8: run_cmd
# 需要导入模块: import subprocess32 [as 别名]
# 或者: from subprocess32 import call [as 别名]
def run_cmd(self, cmd, collect, env=None):
out = []
if self.args.verbose:
self.logr(" CMD: %s" % cmd)
fh = None
if self.args.disable_cmd_redirection or collect == self.Want_Output:
fh = open(self.cov_paths['tmp_out'], 'w')
else:
fh = open(os.devnull, 'w')
if env is None:
subprocess.call(cmd, stdin=None,
stdout=fh, stderr=subprocess.STDOUT, shell=True, executable='/bin/bash')
else:
subprocess.call(cmd, stdin=None,
stdout=fh, stderr=subprocess.STDOUT, shell=True, env=env, executable='/bin/bash')
fh.close()
if self.args.disable_cmd_redirection or collect == self.Want_Output:
with open(self.cov_paths['tmp_out'], 'r') as f:
for line in f:
out.append(line.rstrip('\n'))
return out
示例9: Dedup_Sort
# 需要导入模块: import subprocess32 [as 别名]
# 或者: from subprocess32 import call [as 别名]
def Dedup_Sort(in_bam, mem, threads):
# Mark duplications
st = stage.Stage('picard_mark_duplicates',dbc)
dedup_bam = st.run(run_id,{'.bam':in_bam,'mem':mem})
if (dedup_bam == False):
print "ERROR: picard_mark_duplicates fails"
else:
subprocess.call(["mv",dedup_bam,in_bam])
# Sort bam
st = stage.Stage('sambamba_index',dbc)
st.run(run_id,{'.bam':[in_bam],'threads':threads})
示例10: windows_kill
# 需要导入模块: import subprocess32 [as 别名]
# 或者: from subprocess32 import call [as 别名]
def windows_kill(self):
subprocess.call(['taskkill', '/F', '/IM', 'chromedriver.exe', '/T'])
示例11: _do_exec
# 需要导入模块: import subprocess32 [as 别名]
# 或者: from subprocess32 import call [as 别名]
def _do_exec(self):
return subprocess32.call(self.monitor['args'], timeout=self.monitor['timeout']) == 0
示例12: actualSolve
# 需要导入模块: import subprocess32 [as 别名]
# 或者: from subprocess32 import call [as 别名]
def actualSolve(self, lp):
"""Solve a well formulated lp problem"""
if not self.executable(self.path):
raise PulpSolverError("PuLP: cannot execute "+self.path)
if not self.keepFiles:
pid = os.getpid()
tmpLp = os.path.join(self.tmpDir, "%d-pulp.lp" % pid)
tmpSol = os.path.join(self.tmpDir, "%d-pulp.sol" % pid)
else:
tmpLp = lp.name+"-pulp.lp"
tmpSol = lp.name+"-pulp.sol"
lp.writeLP(tmpLp, writeSOS = 0)
proc = ["glpsol", "--cpxlp", tmpLp, "-o", tmpSol]
if not self.mip: proc.append('--nomip')
proc.extend(self.options)
self.solution_time = clock()
if not self.msg:
proc[0] = self.path
pipe = open(os.devnull, 'w')
if operating_system == 'win':
# Prevent flashing windows if used from a GUI application
startupinfo = subprocess.STARTUPINFO()
startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
rc = subprocess.call(proc, stdout = pipe, stderr = pipe,
startupinfo = startupinfo)
else:
rc = subprocess.call(proc, stdout = pipe, stderr = pipe)
if rc:
raise PulpSolverError("PuLP: Error while trying to execute "+self.path)
else:
if os.name != 'nt':
rc = os.spawnvp(os.P_WAIT, self.path, proc)
else:
rc = os.spawnv(os.P_WAIT, self.executable(self.path), proc)
if rc == 127:
raise PulpSolverError("PuLP: Error while trying to execute "+self.path)
self.solution_time += clock()
if not os.path.exists(tmpSol):
raise PulpSolverError("PuLP: Error while executing "+self.path)
lp.status, values = self.readsol(tmpSol)
lp.assignVarsVals(values)
if not self.keepFiles:
try: os.remove(tmpLp)
except: pass
try: os.remove(tmpSol)
except: pass
return lp.status
示例13: display_config
# 需要导入模块: import subprocess32 [as 别名]
# 或者: from subprocess32 import call [as 别名]
def display_config(args, conf):
'''Display args and conf settings'''
# Don't call validate here as stockfish should be validated from update_config.
stockfish_command = conf_get(conf, "StockfishCommand")
print()
print("### Checking configuration ...")
print()
print("Python: %s (with requests %s)" % (platform.python_version(), requests.__version__))
print("EngineDir: %s" % get_engine_dir(conf))
print("StockfishCommand: %s" % stockfish_command)
print("Key: %s" % (("*" * len(get_key(conf))) or "(none)"))
cores = validate_cores(conf_get(conf, "Cores"))
print("Cores: %d" % cores)
threads = validate_threads_per_process(conf_get(conf, "ThreadsPerProcess"), conf)
instances = max(1, cores // threads)
print("Engine processes: %d (each ~%d threads)" % (instances, threads))
memory = validate_memory(conf_get(conf, "Memory"), conf)
print("Memory: %d MB" % memory)
endpoint = get_endpoint(conf)
warning = "" if endpoint.startswith("https://") else " (WARNING: not using https)"
print("Endpoint: %s%s" % (endpoint, warning))
user_backlog, system_backlog = validate_backlog(conf)
print("UserBacklog: %ds" % user_backlog)
print("SystemBacklog: %ds" % system_backlog)
print("FixedBackoff: %s" % parse_bool(conf_get(conf, "FixedBackoff")))
print()
if conf.has_section("Stockfish") and conf.items("Stockfish"):
print("Using custom UCI options is discouraged:")
for name, value in conf.items("Stockfish"):
if name.lower() == "hash":
hint = " (use --memory instead)"
elif name.lower() == "threads":
hint = " (use --threads-per-process instead)"
else:
hint = ""
print(" * %s = %s%s" % (name, value, hint))
print()
if args.ignored_threads:
print("Ignored deprecated option --threads. Did you mean --cores?")
print()
return cores, threads, instances, memory, user_backlog, system_backlog