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)
def parallel(args):
"""
%prog parallel genome.fasta N
Partition the genome into parts and run separately. This is useful if MAKER
is to be run on the grid.
"""
from jcvi.formats.base import split
p = OptionParser(parallel.__doc__)
p.set_home("maker")
p.set_tmpdir(tmpdir="tmp")
p.set_grid_opts(array=True)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
genome, NN = args
threaded = opts.threaded or 1
tmpdir = opts.tmpdir
mkdir(tmpdir)
tmpdir = get_abs_path(tmpdir)
N = int(NN)
assert 1 <= N < 1000, "Required: 1 < N < 1000!"
outdir = "outdir"
fs = split([genome, outdir, NN])
c = CTLFile("maker_opts.ctl")
c.update_abs_path()
if threaded > 1:
c.update_tag("cpus", threaded)
cwd = os.getcwd()
dirs = []
for name in fs.names:
fn = get_abs_path(name)
bn = op.basename(name)
dirs.append(bn)
c.update_tag("genome", fn)
mkdir(bn)
sh("cp *.ctl {0}".format(bn))
os.chdir(bn)
c.write_file("maker_opts.ctl")
os.chdir(cwd)
jobs = "jobs"
fw = open(jobs, "w")
print("\n".join(dirs), file=fw)
fw.close()
# Submit to grid
ncmds = len(dirs)
runfile = "array.sh"
cmd = op.join(opts.maker_home, "bin/maker")
if tmpdir:
cmd += " -TMP {0}".format(tmpdir)
engine = get_grid_engine()
contents = arraysh.format(jobs, cmd) if engine == "SGE" \
else arraysh_ua.format(N, threaded, jobs, cmd)
write_file(runfile, contents)
if engine == "PBS":
return
# qsub script
outfile = "maker.\$TASK_ID.out"
p = GridProcess(runfile,
outfile=outfile,
errfile=outfile,
arr=ncmds,
grid_opts=opts)
qsubfile = "qsub.sh"
qsub = p.build()
write_file(qsubfile, qsub)