def sh(cmd,
grid=False,
infile=None,
outfile=None,
errfile=None,
background=False,
threaded=None):
"""
simple wrapper for system calls
"""
if grid:
from jcvi.apps.grid import GridProcess
pr = GridProcess(cmd,
infile=infile,
outfile=outfile,
errfile=errfile,
threaded=threaded)
pr.start(path=None)
return 0 # A fake retcode
else:
if infile:
cmd += " < {0} ".format(infile)
if outfile and outfile != "stdout":
cmd += " > {0} ".format(outfile)
if errfile:
cmd += " 2> {0} ".format(errfile)
if background:
cmd += " & "
logging.debug(cmd)
return call(cmd, shell=True)
def sh(cmd, grid=False, infile=None, outfile=None, errfile=None,
append=False, background=False, threaded=None, log=True,
grid_opts=None, shell="/bin/bash"):
"""
simple wrapper for system calls
"""
if not cmd:
return 1
if grid:
from jcvi.apps.grid import GridProcess
pr = GridProcess(cmd, infile=infile, outfile=outfile, errfile=errfile,
threaded=threaded, grid_opts=grid_opts)
pr.start()
return pr.jobid
else:
if infile:
cat = "cat"
if infile.endswith(".gz"):
cat = "zcat"
cmd = "{0} {1} | ".format(cat, infile) + cmd
if outfile and outfile != "stdout":
if outfile.endswith(".gz"):
cmd += " | gzip"
tag = ">"
if append:
tag = ">>"
cmd += " {0} {1} ".format(tag, outfile)
if errfile:
cmd += " 2> {0} ".format(errfile)
if background:
cmd += " & "
if log:
logging.debug(cmd)
return call(cmd, shell=True, executable=shell)
def sh(cmd,
grid=False,
infile=None,
outfile=None,
errfile=None,
append=False,
background=False,
threaded=None,
log=True,
grid_opts=None,
shell="/bin/bash"):
"""
simple wrapper for system calls
"""
if not cmd:
return 1
if grid:
from jcvi.apps.grid import GridProcess
pr = GridProcess(cmd,
infile=infile,
outfile=outfile,
errfile=errfile,
threaded=threaded,
grid_opts=grid_opts)
pr.start()
return pr.jobid
else:
if infile:
cat = "cat"
if infile.endswith(".gz"):
cat = "zcat"
cmd = "{0} {1} |".format(cat, infile) + cmd
if outfile and outfile != "stdout":
if outfile.endswith(".gz"):
cmd += " | gzip"
tag = ">"
if append:
tag = ">>"
cmd += " {0}{1}".format(tag, outfile)
if errfile:
if errfile == outfile:
errfile = "&1"
cmd += " 2>{0}".format(errfile)
if background:
cmd += " &"
if log:
logging.debug(cmd)
return call(cmd, shell=True, executable=shell)
def sh(cmd, grid=False, infile=None, outfile=None, errfile=None,
background=False):
"""
simple wrapper for system calls
"""
if grid:
from jcvi.apps.grid import GridProcess
pr = GridProcess(cmd, infile=infile, outfile=outfile, errfile=errfile)
pr.start(path=None)
return 0 # A fake retcode
else:
if infile:
cmd += " < {0} ".format(infile)
if outfile and outfile != "stdout":
cmd += " > {0} ".format(outfile)
if errfile:
cmd += " 2> {0} ".format(errfile)
if background:
cmd += " & "
logging.debug(cmd)
return call(cmd, shell=True)