Commit 383e738a authored by Celine Mercier's avatar Celine Mercier

Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git

parents 86071d30 61576331
#!/usr/local/bin/python3.4
'''
obi -- shortdesc
obi is a description
It defines classes_and_methods
@author: user_name
@copyright: 2014 organization_name. All rights reserved.
@license: license
@contact: user_email
@deffield updated: Updated
'''
import sys
import pkgutil
import argparse
import logging
import json
default_config = {
'obi' : { 'log' : True,
'loglevel' : 'INFO',
'version' : False,
'progress' : True
}
}
from obitools3 import command
from obitools3.version import version
__all__ = []
__version__ = version
__date__ = '2014-09-28'
__updated__ = '2014-09-28'
DEBUG = 1
TESTRUN = 0
PROFILE = 0
def loadCommand(name,loader):
'''
Load a command module from its name and an ImpLoader
This function is for internal use
@param name: name of the module
@type name: str
@param loader: the module loader
@type loader: ImpLoader
@return the loaded module
@rtype: module
'''
module = loader.find_module(name).load_module(name)
return module
def getCommandsList():
'''
Returns the list of sub-commands available to the main `obi` command
@return: a dict instance with key corresponding to each command and
value corresponding to the module
@rtype: dict
'''
cmds = dict((x[1],loadCommand(x[1],x[0]))
for x in pkgutil.iter_modules(command.__path__)
if not x[2])
return cmds
def getLogger(config):
'''
Returns the logger as defined by the command line option
or by the config file
:param config:
'''
output = config['obi']['outputfilename']
level = config['obi']['loglevel']
logfile= config['obi']['log']
rootlogger = logging.getLogger()
logFormatter = logging.Formatter("%(asctime)s [%(levelname)-5.5s] %(message)s")
stderrHandler = logging.StreamHandler(sys.stderr)
stderrHandler.setFormatter(logFormatter)
rootlogger.addHandler(stderrHandler)
if logfile:
fileHandler = logging.FileHandler("%s.log" % output)
fileHandler.setFormatter(logFormatter)
rootlogger.addHandler(fileHandler)
try:
loglevel = getattr(logging, level)
except:
loglevel = logging.INFO
rootlogger.setLevel(loglevel)
config['obi']['logger']=rootlogger
return rootlogger
class ObiParser(argparse.ArgumentParser):
def error(self, message):
sys.stderr.write('error: %s\n' % message)
self.print_help()
sys.exit(2)
def buildArgumentParser():
parser = ObiParser()
parser.add_argument('--version', dest='obi:version',
action='store_true',
default=False,
help='Print the version of the OBITools')
parser.add_argument('--no-log', dest='obi:log',
action='store_false',
default=None,
help='Do not create a logfile for the data analyze')
parser.add_argument('--no-progress', dest='obi:progress',
action='store_false',
default=None,
help='Do not print the progress bar during analyzes')
subparsers = parser.add_subparsers(title='subcommands',
description='valid subcommands',
help='additional help')
commands = getCommandsList()
for c in commands:
module = commands[c]
if hasattr(module, "run"):
if hasattr(module, "__title__"):
sub = subparsers.add_parser(c,help=module.__title__)
else:
sub = subparsers.add_parser(c)
if hasattr(module, "addOptions"):
module.addOptions(sub)
sub.set_defaults(**{'obi:module' : module})
return parser
def buildDefaultConfiguration():
global default_config
commands = getCommandsList()
for c in commands:
module = commands[c]
assert hasattr(module, "run")
if hasattr(module, 'default_config'):
default_config[c]=module.default_config
else:
default_config[c]={}
return default_config
def getConfiguration():
global default_config
if '__done__' in default_config:
return default_config
parser = buildArgumentParser()
options = vars(parser.parse_args())
config = buildDefaultConfiguration()
for k in options:
section,key = k.split(':')
s = config[section]
if options[k] is not None:
s[key]=options[k]
if config['obi']['version']:
print("The OBITools - Version %s" % __version__)
sys.exit(0)
if not 'module' in config['obi']:
print('\nError: No obi command specified',file=sys.stderr)
parser.print_help()
sys.exit(2)
if config['obi']['outputfilename'] is None:
config['obi']['outputfilename']=config['obi']['indexfilename']
getLogger(config)
config['__done__']=True
return config
if __name__ =="__main__":
config = getConfiguration()
config['obi']['module'].run(config)
\ No newline at end of file
'''
Created on 8 mars 2016
@author: coissac
'''
__title__="Counts sequences in a sequence set"
default_config = { 'countmode' : None
}
def addOptions(parser):
parser.add_argument(dest='obi:input', metavar='obi:input',
nargs='?',
default=None,
help='input data set' )
group=parser.add_option_group('Obicount specific options')
group.add_option('-s','--sequence',
action="store_true", dest="count:sequence",
default=False,
help="Prints only the number of sequence records."
)
group.add_option('-a','--all',
action="store_true", dest="count:all",
default=False,
help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False)."
)
def run(config):
# The code of my command
pass
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