def main():
# Setup the command line arguments.
optp = OptionParser()
# Output verbosity options
optp.add_option('-q', '--quiet', help='set logging to ERROR',
action='store_const', dest='loglevel',
const=logging.ERROR, default=logging.INFO)
optp.add_option('-d', '--debug', help='set logging to DEBUG',
action='store_const', dest='loglevel',
const=logging.DEBUG, default=logging.INFO)
optp.add_option('-v', '--verbose', help='set logging to COMM',
action='store_const', dest='loglevel',
const=5, default=logging.INFO)
# Option for hash to download
optp.add_option("-i", "--ioc", dest="ioc",
help="The hash, ip, or domain of the ioc you want to check")
opts, args = optp.parse_args()
# Prompt if the user disn't give an ioc
if opts.ioc is None:
opts.ioc = raw_input("What's your IOC (Hash, ip, domain)? ")
results = checkSS(opts.ioc)
print results
def getProgOptions():
from optparse import OptionParser, make_option
option_list = [
make_option("-i", "--in-seq",
action="append", type="string",dest="inSeq"),
make_option("-o", "--out-name",
action="store", type="string",dest="outName"),
make_option("-s", "--num-splits",
action="store", type="int",dest="nSplits",default=3),
make_option("-m", "--min-samp-count",
action="store", type="int",dest="minSampCount",default=100),
make_option("-t", "--max-samp-seq",
action="store", type="int",dest="maxSampCountPerSeq"),
make_option("-l", "--samp-len",
action="store", type="int",dest="sampLen",default=1000),
make_option("-f", "--samp-offset",
action="store", type="int",dest="sampOffset",default=0),
make_option("-d", "--make-other",
action="store_true", dest="makeOther",default=False),
make_option("-a", "--alphabet",
action="store", type="choice",choices=("dna","protein"),
dest="alphabet",default="dna"),
make_option("-e", "--degen-len",
action="store", type="int",dest="degenLen",default=1),
]
parser = OptionParser(usage = "usage: %prog [options]",option_list=option_list)
(options, args) = parser.parse_args()
return options,args
def process_options(debugger_name, pkg_version, sys_argv, option_list=None):
"""Handle debugger options. Set `option_list' if you are writing
another main program and want to extend the existing set of debugger
options.
The options dicionary from opt_parser is return. sys_argv is
also updated."""
usage_str="""%prog [debugger-options] [python-script [script-options...]]
Runs the extended python debugger"""
# serverChoices = ('TCP','FIFO', None)
optparser = OptionParser(usage=usage_str, option_list=option_list,
version="%%prog version %s" % pkg_version)
optparser.add_option("-F", "--fntrace", dest="fntrace",
action="store_true", default=False,
help="Show functions before executing them. " +
"This option also sets --batch")
optparser.add_option("--basename", dest="basename",
action="store_true", default=False,
help="Filenames strip off basename, "
"(e.g. for regression tests)")
optparser.add_option("--different", dest="different",
action="store_true", default=True,
help="Consecutive stops should have different "
"positions")
optparser.disable_interspersed_args()
sys.argv = list(sys_argv)
(opts, sys.argv) = optparser.parse_args()
dbg_opts = {}
return opts, dbg_opts, sys.argv
def main():
"""Run the application from outside the module - used for
deploying as frozen app"""
import sys, os
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-f", "--file", dest="msgpack",
help="Open a dataframe as msgpack", metavar="FILE")
parser.add_option("-p", "--project", dest="projfile",
help="Open a dataexplore project file", metavar="FILE")
parser.add_option("-i", "--csv", dest="csv",
help="Open a csv file by trying to import it", metavar="FILE")
parser.add_option("-t", "--test", dest="test", action="store_true",
default=False, help="Run a basic test app")
opts, remainder = parser.parse_args()
if opts.test == True:
app = TestApp()
else:
if opts.projfile != None:
app = DataExplore(projfile=opts.projfile)
elif opts.msgpack != None:
app = DataExplore(msgpack=opts.msgpack)
elif opts.csv != None:
app = DataExplore()
t = app.getCurrentTable()
t.importCSV(opts.csv)
else:
app = DataExplore()
app.mainloop()
def main(args=None):
# parse the command line
from optparse import OptionParser
parser = OptionParser(description=__doc__)
for key in choices:
parser.add_option('--%s' % key, dest=key,
action='store_true', default=False,
help="display choices for %s" % key)
options, args = parser.parse_args()
# args are JSON blobs to override info
if args:
# lazy import
import json
for arg in args:
if _os.path.exists(arg):
string = file(arg).read()
else:
string = arg
update(json.loads(string))
# print out choices if requested
flag = False
for key, value in options.__dict__.items():
if value is True:
print '%s choices: %s' % (key, ' '.join([str(choice)
for choice in choices[key]]))
flag = True
if flag:
return
# otherwise, print out all info
for key, value in info.items():
print '%s: %s' % (key, value)
def _getArgs():
parser = OptionParser(usage="Train HTM Spatial Pooler")
parser.add_option("-d",
"--dataSet",
type=str,
default='randomSDR',
dest="dataSet",
help="DataSet Name, choose from sparse, correlated-input"
"bar, cross, image")
parser.add_option("-b",
"--boosting",
type=int,
default=1,
dest="boosting",
help="Whether to use boosting")
parser.add_option("-e",
"--numEpochs",
type=int,
default=100,
dest="numEpochs",
help="number of epochs")
parser.add_option("--spatialImp",
type=str,
default="cpp",
dest="spatialImp",
help="spatial pooler implementations: py, c++, or "
"monitored_sp")
(options, remainder) = parser.parse_args()
print options
return options, remainder
def main(argv=None):
"""Main entry point for the script"""
ret_code = 0
if argv is None:
argv = sys.argv
parser = OptionParser()
parser.add_option("-f", "--file", action="store", type="string",
dest="filepath", default="/var/log/asterisk/refs",
help="The full path to the refs file to process")
(options, args) = parser.parse_args(argv)
if not os.path.isfile(options.filepath):
print("File not found: %s" % options.filepath, file=sys.stderr)
return -1
try:
process_file(options)
except (KeyboardInterrupt, SystemExit, IOError):
print("File processing cancelled", file=sys.stderr)
return -1
return ret_code
def main():
"""gterm-aware matplotlib demo"""
setup()
import matplotlib.pyplot as plt
from optparse import OptionParser
usage = "usage: %prog [--animate]"
parser = OptionParser(usage=usage)
parser.add_option("", "--animate",
action="store_true", dest="animate", default=False,
help="Simple animation demo")
(options, args) = parser.parse_args()
fmt = "png"
if options.animate:
plt.plot([1,2,3,2,3,1])
show(overwrite=False, format=fmt, title="Simple animation")
n = 10
dx = 5.0/n
for j in range(1,n):
time.sleep(0.5)
plt.plot([1,2,3,2,3,1+j*dx])
show(overwrite=True, format=fmt)
else:
plt.plot([1,2,3,2,3,0])
show(overwrite=False, format=fmt, title="Simple plot")
def make_cli_parser():
"""
Creates the command line interface parser.
"""
usage = "\n".join([
"""\
python %prog [OPTIONS] FASTAFILE1 FASTAFILE2 ...
ARGUMENTS:
FASTAFILE1, FASTAFILE2, ...: paths to one or more FASTA formatted files
""",
__doc__
])
cli_parser = OptionParser(usage)
cli_parser.add_option(
'-o', '--outfile', default=OUTFILE_NAME,
help="path to output file [Default: %default]"
)
cli_parser.add_option(
'-b', '--barrelon', action='store_true',
help="ignore possible errors in parsing"
)
return cli_parser
def setupParser(self, argv):
usage = "usage: %prog [options]"
parser = OptionParser(usage)
parser.add_option('-o', '--output-dir',
action='store', dest='outputDir', default='./restdoc-output',
help='The output directory for the API documentation files.')
parser.add_option('-f', '--format',
action='store', dest='format', default=0,
help='The output format (MediaWiki). [Default: MediaWiki].')
parser.add_option('-p', '--private-api',
action='store_true', dest='privateApi', default=False,
help='Generates private API documentation. [Default: False]')
parser.add_option('-u', '--upload-documentation',
action='store_true', dest='uploadDocumentation', default=False,
help='Uploads the documentation to the Bitmunk wiki. ' + \
'[Default: False]')
self.options, args = parser.parse_args(argv)
largs = parser.largs
return (self.options, args, largs)
def main():
parser = OptionParser(usage="%prog [options] jobfile|-",
description=__doc__, version='%prog version 0.1')
parser.add_option("-n", "--nb-procs", dest="nb_procs", type="int",
default=DEFAULT_PROCESSES,
help=("By default the number of concurent processes to "
"run is equal to the number of CPUs "
"(Default: %default)")
)
(opts, spillover) = parser.parse_args()
if len(spillover) != 1:
parser.error('Invalid arguments.')
if opts.nb_procs < 2:
parser.error("There is no point of using that program if you are not "
"running anything in parallel.")
if spillover[0] == '-':
jobfd = sys.stdin
else:
try:
jobfd = open(spillover[0])
except IOError:
parser.error("Job file '%s' open error" % spillover[0])
run_pexec(jobfd, opts.nb_procs)
def parse_options():
parser = OptionParser()
parser.add_option("-f", "--file",
dest="filename", default="/etc/sssd/sssd.conf",
help="Set input file to FILE", metavar="FILE")
parser.add_option("-o", "--outfile",
dest="outfile", default=None,
help="Set output file to OUTFILE", metavar="OUTFILE")
parser.add_option("", "--no-backup", action="store_false",
dest="backup", default=True,
help="""Do not provide backup file after conversion.
The script copies the original file with the suffix .bak
by default""")
parser.add_option("-v", "--verbose", action="store_true",
dest="verbose", default=False,
help="Be verbose")
(options, args) = parser.parse_args()
if len(args) > 0:
print >>sys.stderr, "Stray arguments: %s" % ' '.join([a for a in args])
return None
# do the conversion in place by default
if not options.outfile:
options.outfile = options.filename
return options
def main(argv=None):
if argv is None:
argv = sys.argv
parser = OptionParser()
parser.add_option("-k", "--key", dest="key",
help="your Giant Bomb API key")
opts, args = parser.parse_args()
if opts.key is None:
print >>sys.stderr, "Option --key is required"
return 1
query = ' '.join(args)
Bombject.api_key = opts.key
search = GameResult.get('/search/').filter(resources='game')
search = search.filter(query=query)
if len(search.results) == 0:
print "No results for %r" % query
elif len(search.results) == 1:
(game,) = search.results
print "## %s ##" % game.name
print
print game.summary
else:
print "## Search results for %r ##" % query
for game in search.results:
print game.name
return 0
def __init__(self, **kwargs):
OptionParser.__init__(self, **kwargs)
self.add_option("-m", "--masterMode", action="store_true", dest="masterMode",
help="Run the script in master mode.", default=False)
self.add_option("--noPrompts", action="store_true", dest="noPrompts",
help="Uses default answers (intended for CLOUD TESTS only!).", default=False)
self.add_option("--manifestFile", action="store", type="string", dest="manifestFile",
help="A JSON file in the form of test_manifest.json (the default).")
self.add_option("-b", "--browser", action="store", type="string", dest="browser",
help="The path to a single browser (right now, only Firefox is supported).")
self.add_option("--browserManifestFile", action="store", type="string",
dest="browserManifestFile",
help="A JSON file in the form of those found in resources/browser_manifests")
self.add_option("--reftest", action="store_true", dest="reftest",
help="Automatically start reftest showing comparison test failures, if there are any.",
default=False)
self.add_option("--port", action="store", dest="port", type="int",
help="The port the HTTP server should listen on.", default=8080)
self.add_option("--unitTest", action="store_true", dest="unitTest",
help="Run the unit tests.", default=False)
self.add_option("--fontTest", action="store_true", dest="fontTest",
help="Run the font tests.", default=False)
self.add_option("--noDownload", action="store_true", dest="noDownload",
help="Skips test PDFs downloading.", default=False)
self.add_option("--statsFile", action="store", dest="statsFile", type="string",
help="The file where to store stats.", default=None)
self.add_option("--statsDelay", action="store", dest="statsDelay", type="int",
help="The amount of time in milliseconds the browser should wait before starting stats.", default=10000)
self.set_usage(USAGE_EXAMPLE)
def __init__(self):
gr.top_block.__init__(self)
usage="%prog: [options] output_filename"
parser = OptionParser(option_class=eng_option, usage=usage)
parser.add_option("-I", "--audio-input", type="string", default="",
help="pcm input device name. E.g., hw:0,0 or /dev/dsp")
parser.add_option("-r", "--sample-rate", type="eng_float", default=48000,
help="set sample rate to RATE (48000)")
parser.add_option("-N", "--nsamples", type="eng_float", default=None,
help="number of samples to collect [default=+inf]")
(options, args) = parser.parse_args ()
if len(args) != 1:
parser.print_help()
raise SystemExit, 1
filename = args[0]
sample_rate = int(options.sample_rate)
src = audio.source (sample_rate, options.audio_input)
dst = gr.file_sink (gr.sizeof_float, filename)
if options.nsamples is None:
self.connect((src, 0), dst)
else:
head = gr.head(gr.sizeof_float, int(options.nsamples))
self.connect((src, 0), head, dst)
def ParseInputs():
global DOMAIN_PAIRS
usage = """usage: %prog -d <domain> -u <admin_user> -p <admin_pass>\n"""
parser = OptionParser()
parser.add_option("-u", dest="admin_user", help="admin user")
parser.add_option("-p", dest="admin_pass", help="admin pass")
parser.add_option("-d", dest="domain", help="Domain name")
parser.add_option("-n", dest="nick_domain",
help="The domain of the nick that should exist.",)
parser.add_option("--apply", action="store_true", dest="apply",
help="""If present, changes will be applied, otherwise
will run in dry run mode with no changes made""")
(options, args) = parser.parse_args()
if options.admin_user is None:
print "-u (admin user) is required"
sys.exit(1)
if options.admin_pass is None:
print "-p (admin password) is required"
sys.exit(1)
if (options.domain and not options.nick_domain) or (options.nick_domain and not options.domain):
print "Both -d and -n need to be given"
sys.exit(1)
if not options.domain and not options.nick_domain and not DOMAIN_PAIRS:
print "No domain pairs given"
sys.exit(1)
return options
def parse_options():
""" Options parser. """
parser = OptionParser(option_class=eng_option, usage="%prog: [options]")
parser.add_option("-s", "--servername", type="string", default="localhost",
help="Server hostname")
(options, args) = parser.parse_args()
return options
def main():
parser = OptionParser(usage="usage:%prog [options] filepath")
parser.add_option("-p", "--port",
action="store", type="string", default="", dest="port")
(options, args) = parser.parse_args()
port = options.port
print port
if not port:
port = utils.config.get("global", "port")
debug_mode = int(utils.config.get('global', 'debug'))
sys.stderr.write("listen server on port %s ...\n" % port)
settings = dict(
debug=True if debug_mode else False,
cookie_secret="e446976943b4e8442f099fed1f3fea28462d5832f483a0ed9a3d5d3859f==78d",
session_secret="3cdcb1f00803b6e78ab50b466a40b9977db396840c28307f428b25e2277f1bcc",
session_timeout=600,
store_options={
'redis_host': '127.0.0.1',
'redis_port': 6379,
'redis_pass': '',
}
)
application = HandlersApplication(handler, **settings)
server = tornado.httpserver.HTTPServer(application)
server.bind(port)
server.start(1 if debug_mode else 15)
tornado.ioloop.IOLoop.instance().start()
def main():
from optparse import OptionParser
parser = OptionParser()
parser.add_option('-c', type='int', dest='concurrency', default=DEFAULT_CONCURRENCY,
help='Number of multiple requests to make')
parser.add_option('-s', type='int', dest='seconds', default=DEFAULT_SECONDS,
help='Number of seconds to perform')
parser.add_option("--mode", dest="mode", default=None)
options, args = parser.parse_args()
#run tests
if 'test' == options.mode:
test_parse_http_load_result()
return
if 1 != len(args):
parser.print_help()
return
assert 1 <= options.concurrency <= 100
assert 1 <= options.seconds <= 100
#run bench
old_sys_stderr = sys.stderr
sys.stderr = StringIO()
try:
run_bench(args[0], options.seconds, options.concurrency)
except Exception, e:
print e
import traceback
print traceback.format_exc()
def __init__(self, **kwargs):
OptionParser.__init__(self, **kwargs)
self.add_option('--dz-url',
action='store',
dest='datazilla_url',
default='https://datazilla.mozilla.org',
metavar='str',
help='datazilla server url (default: %default)')
self.add_option('--dz-project',
action='store',
dest='datazilla_project',
metavar='str',
help='datazilla project name')
self.add_option('--dz-branch',
action='store',
dest='datazilla_branch',
metavar='str',
help='datazilla branch name')
self.add_option('--dz-key',
action='store',
dest='datazilla_key',
metavar='str',
help='oauth key for datazilla server')
self.add_option('--dz-secret',
action='store',
dest='datazilla_secret',
metavar='str',
help='oauth secret for datazilla server')
self.add_option('--sources',
action='store',
dest='sources',
metavar='str',
help='path to sources.xml containing project revisions')
def main(self,args=None):
"""
meant to be called
if __name__ == '__main__':
MyApplication().main()
but lino.runscript calls it with args=sys.argv[:2] (command-line
arguments are shifted by one)
"""
if args is None:
args = sys.argv[1:]
p = OptionParser(
usage=self.usage,
description=self.description)
self.setupOptionParser(p)
try:
options,args = p.parse_args(args)
self.applyOptions(options,args)
return self.run(self.console)
except UsageError,e:
p.print_help()
return -1
def cli_main(self,argv):
with self: # so the sys.path was modified appropriately
# I believe there's no performance hit loading these here when
# CLI--it would load everytime anyway.
from StringIO import StringIO
from calibre.library import db
from calibre_plugins.fanficfare_plugin.fanficfare.cli import main as fff_main
from calibre_plugins.fanficfare_plugin.prefs import PrefsFacade
from calibre.utils.config import prefs as calibre_prefs
from optparse import OptionParser
parser = OptionParser('%prog --run-plugin '+self.name+' -- [options] <storyurl>')
parser.add_option('--library-path', '--with-library', default=None, help=_('Path to the calibre library. Default is to use the path stored in the settings.'))
# parser.add_option('--dont-notify-gui', default=False, action='store_true',
# help=_('Do not notify the running calibre GUI (if any) that the database has'
# ' changed. Use with care, as it can lead to database corruption!'))
pargs = [x for x in argv if x.startswith('--with-library') or x.startswith('--library-path')
or not x.startswith('-')]
opts, args = parser.parse_args(pargs)
fff_prefs = PrefsFacade(db(path=opts.library_path,
read_only=True))
fff_main(argv[1:],
parser=parser,
passed_defaultsini=StringIO(get_resources("fanficfare/defaults.ini")),
passed_personalini=StringIO(fff_prefs["personal.ini"]))
def main () :
usage = "./app/python/arc2warc.py [OPTIONS] ARC-FILES "
parser = OptionParser(usage)
parser.add_option("-c", "--compressed", dest="cmode",
action="store_true", help="compressed outpout WARC FILE")
parser.add_option("-t", "--tempdir", dest="tmpdir",
help="Temporary working directory", default="./")
parser.add_option("-v","--verbose",
action="store_true",dest="verbose" , default=False,
help="print more information")
(options, args) = parser.parse_args()
if not ( len (args) > 0 ):
parser.error(" Please give one or more arcs to convert")
for fname in args:
ofname = guessname( fname , options.cmode )
if options.verbose:
print 'Converting %s to %s' % ( fname , ofname )
convert( fname , ofname , options.tmpdir , options.cmode )
if options.verbose:
print 'Done'
return
def main():
os.chdir(os.path.dirname(os.path.realpath(__file__)))
parser = OptionParser()
parser.add_option(
"-d",
dest="debug",
action="store_true",
default=False,
help="Enable debug mode (different starting board configuration)",
)
parser.add_option("-t", dest="text", action="store_true", default=False, help="Use text-based GUI")
parser.add_option("-o", dest="old", action="store_true", default=False, help="Use old graphics in pygame GUI")
parser.add_option(
"-p",
dest="pauseSeconds",
metavar="SECONDS",
action="store",
default=0,
help="Sets time to pause between moves in AI vs. AI games (default = 0)",
)
(options, args) = parser.parse_args()
game = PythonChessMain(options)
game.SetUp(options)
game.MainLoop()
def main():
description = ( "This application generates .h and .ld files for symbols defined in input file. "
"The input symbols file can be generated using nm utility like this: "
"esp32-ulp-nm -g -f posix <elf_file> > <symbols_file>" );
parser = OptionParser(description=description)
parser.add_option("-s", "--symfile", dest="symfile",
help="symbols file name", metavar="SYMFILE")
parser.add_option("-o", "--outputfile", dest="outputfile",
help="destination .h and .ld files name prefix", metavar="OUTFILE")
(options, args) = parser.parse_args()
if options.symfile is None:
parser.print_help()
return 1
if options.outputfile is None:
parser.print_help()
return 1
with open(options.outputfile + ".h", 'w') as f_h, \
open(options.outputfile + ".ld", 'w') as f_ld, \
open(options.symfile) as f_sym: \
gen_ld_h_from_sym(f_sym, f_ld, f_h)
return 0
def main():
p = OptionParser()
options, args = p.parse_args()
if len(args) != 1:
p.error("no valid directory given")
inp = args[0]
outp = inp + ".npz"
files = []
for dirpath, dirnames, filenames in os.walk(inp):
for fn in filenames:
if fn.endswith('.txt'):
files.append(
(dirpath[len(inp)+1:] + '/' + fn[:-4],
os.path.join(dirpath, fn)))
data = {}
for key, fn in files:
key = key.replace('/', '-').strip('-')
try:
data[key] = np.loadtxt(fn)
except ValueError:
print("Failed to load", fn)
savez_compress(outp, **data)
def main(argv):
"""Flag options, automatically adds a -h/--help flag with this information."""
parser = OptionParser()
parser.add_option("-f", "--file", dest="filename", help="read mountpoints from FILE", metavar="FILE")
parser.add_option("-o", "--output", dest="output", help="dump drive information to FILE", metavar="FILE")
parser.add_option("-p", "--prompt", dest="prompt", help="specify drive information before adding to database", action="store_true")
parser.add_option("-l", "--location", dest="location", help="add hard drives to groups (boxes)", action="store_true")
(options, args) = parser.parse_args()
filename = options.filename
try:
if options.location:
o = Organization()
o.prompt()
if filename == None:
# default file to read drives from
filename = "drives.in"
#TODO: add username/password table
username = raw_input("Enter username: ")
while not username:
username = raw_input("Enter username: ")
parse_drives(filename, username, options.output, options.prompt)
except IOError:
print "No file to read drives from. Please create a \'drives.in\' file to place the drives in, or specify a file with the -f flag."
def main():
atexit.register(fabric_cleanup, True)
parser = OptionParser(usage="%prog RELEASE_DIR DESTINATION")
(options, args) = parser.parse_args(sys.argv[1:])
comm_obj = _CommObj()
if len(args) != 2:
parser.print_help()
sys.exit(-1)
if not os.path.isdir(args[0]):
print "release directory %s not found" % args[0]
sys.exit(-1)
destparts = args[1].split(':', 1)
if len(destparts)==1: # it's a local release test area
if not os.path.isdir(args[1]):
_setup_local_release_dir(args[1])
comm_obj.put = shutil.copy
comm_obj.put_dir = shutil.copytree
comm_obj.run = local
_push_release(args[0], args[1], comm_obj)
else: # assume args[1] is a remote host:destdir
comm_obj.put = put
comm_obj.put_dir = put_dir
comm_obj.run = run
home = destparts[1]
with settings(host_string=destparts[0]):
_push_release(args[0], home, comm_obj)
def main():
PROG = os.path.basename(os.path.splitext(__file__)[0])
description = """Scan claims files"""
parser = OptionParser(option_class=MultipleOption,
usage='usage: %prog claims_file, claims_file, ...',
version='%s %s' % (PROG, VERSION),
description=description)
if len(sys.argv) == 1:
parser.parse_args(['--help'])
args = parser.parse_args()
p2k = {}
k2p = {}
try:
with open('claimants.csv') as csv_file:
for line in csv.reader(csv_file, dialect="excel"):
p2k[line[0]] = line[1]
k2p[line[1]] = line[0]
except IOError:
pass
for filename in args[1]:
with open(filename+'_masked.csv', 'wb') as cf:
outfile = csv.writer(cf, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
analyze_file(filename, outfile, p2k, k2p)
print len(p2k), len(k2p)
with open('claimants.csv', 'wb') as cf:
cout = csv.writer(cf, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
for p in p2k:
cout.writerow([p, p2k[p]])
def main(argv):
optparse_usage = 'reaction_table.py -i <input_paths> -g <deltaG_path> -f <table_format> -r <root_dir>'
parser = OptionParser(usage=optparse_usage)
parser.add_option("-i", "--inputpaths", action="store", type="string",
dest="input_path", help='The input file is the kegg_reaction.tsv')
parser.add_option("-g", "--deltaGpaths", action="store", type="string",
dest="deltaG_path", help='The input file is the Info_deltaG.csv')
parser.add_option("-r", "--rootDir", action="store", type="string",
dest="root_dir", help='The root directory. All files are generated here.')
parser.add_option("-f", "--tableFormat", action="store", type="string",
dest="format_path", help='The different number that you have given before.')
(options, args) = parser.parse_args()
if options.input_path:
input_path = os.path.abspath(options.input_path)
else:
print 'Error: please provide proper input file name'
if options.format_path:
format_path = os.path.abspath(options.format_path)
else:
print 'Error: please provide proper input file name'
if options.deltaG_path:
deltaG_path = os.path.abspath(options.deltaG_path)
else:
print 'Error: please provide proper input file name'
if options.root_dir:
root_dir = os.path.abspath(options.root_dir)
else:
print 'ERROR: please provide proper root direcotory'
# Run the funtion
make_file(input_path,deltaG_path, format_path, root_dir)
