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

python/obi.py

@@ -0,0 +1,228 @@
+#!/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)
+    
+    
+    

python/obitools3/command/count.py

@@ -0,0 +1,36 @@
+'''
+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