Add argument to give a configfile

PanACoTA/subcommands/all_modules.py

@@ -175,6 +175,9 @@ def build_parser(parser):
 
     # Create command-line parser for all options and arguments to give
     general = parser.add_argument_group("General arguments")
+    general.add_argument("-c", dest="configfile",
+                          help=("Path to your configuration file, defining values of parameters.")
+                          )
     general.add_argument("-o", dest="outdir", required=True,
                           help=("Path to your output folder, where all results "
                                 "from all 6 modules will be saved.")
@@ -305,7 +308,6 @@ def check_args(parser, argv):
     # If a bool argument (quiet, mixed, multi, prodigal_only) is not in the user command-line,
     # it still exists in argv but is set to False -> ignore it to replace by info from
     # config file if any, or default otherwise
-    argv.conffile = "configfile.ini"
     dict_argv = {key:val for key,val in vars(argv).items() if val is not None and val != False}
 
     final_dict = {}
@@ -359,9 +361,14 @@ def get_prepare(dict_argv):
     Check that arguments given for prepare step are compatible
     """
     # Get arguments from config file and add them (overwrite if needed)
-    conf_conffile = utils_argparse.Conf_all_parser(dict_argv['conffile'], sections=["prepare"])
+    if not "configfile" in dict_argv:
+        conf_conffile = utils_argparse.Conf_all_parser("",["prepare"])
+    else:
+        conf_conffile = utils_argparse.Conf_all_parser(dict_argv['configfile'],
+                                                       sections=["prepare"])
     # Add arguments from commandline
     conf_conffile.update(dict_argv, "prepare")
+    # Add default arguments if not found in comd line nor config file
     defaults = {"verbose": 0, "threads": 1, "cutn": 5, "l90": 100, "nbcont":999,
                 "min_id": 0.8, "levels": "", "quiet": False, "ncbi_species": "",
                 "ncbi_species_taxid": "", "tmp_dir": "", "db_dir": "",
@@ -388,7 +395,11 @@ def get_annotate(dict_argv):
     Check that arguments given for prepare step are compatible
     """
     # Get arguments from config file and add them (overwrite if needed)
-    conf_conffile = utils_argparse.Conf_all_parser(dict_argv['conffile'], sections=["annotate"])
+    if not "configfile" in dict_argv:
+        conf_conffile = utils_argparse.Conf_all_parser("",["annotate"])
+    else:
+        conf_conffile = utils_argparse.Conf_all_parser(dict_argv['configfile'],
+                                                       sections=["annotate"])
     # Add arguments from commandline
     conf_conffile.update(dict_argv, "annotate")
     if "date" not in dict(conf_conffile["annotate"]):
@@ -417,7 +428,11 @@ def get_pangenome(dict_argv):
     Check that arguments given for prepare step are compatible
     """
     # Get arguments from config file and add them (overwrite if needed)
-    conf_conffile = utils_argparse.Conf_all_parser(dict_argv['conffile'], sections=["pangenome"])
+    if not "configfile" in dict_argv:
+        conf_conffile = utils_argparse.Conf_all_parser("",["pangenome"])
+    else:
+        conf_conffile = utils_argparse.Conf_all_parser(dict_argv['configfile'],
+                                                       sections=["pangenome"])
     # Add arguments from commandline
     conf_conffile.update(dict_argv, "pangenome")
     # Add default arguments if not found in commandline nor config file
@@ -437,7 +452,11 @@ def get_corepers(dict_argv):
     Check that arguments given for prepare step are compatible
     """
     # Get arguments from config file and add them (overwrite if needed)
-    conf_conffile = utils_argparse.Conf_all_parser(dict_argv['conffile'], sections=["corepers"])
+    if not "configfile" in dict_argv:
+        conf_conffile = utils_argparse.Conf_all_parser("",["corepers"])
+    else:
+        conf_conffile = utils_argparse.Conf_all_parser(dict_argv['configfile'],
+                                                       sections=["corepers"])
     # Add arguments from commandline
     conf_conffile.update(dict_argv, "corepers")
     # Add default arguments if not found in commandline nor config file
@@ -460,7 +479,10 @@ def get_tree(dict_argv):
     Check that arguments given for prepare step are compatible
     """
     # Get arguments from config file and add them (overwrite if needed)
-    conf_conffile = utils_argparse.Conf_all_parser(dict_argv['conffile'], sections=["tree"])
+    if not "configfile" in dict_argv:
+        conf_conffile = utils_argparse.Conf_all_parser("",["tree"])
+    else:
+        conf_conffile = utils_argparse.Conf_all_parser(dict_argv['configfile'], sections=["tree"])
     # Add arguments from commandline
     conf_conffile.update(dict_argv, "tree")
     # Add default arguments if not found in commandline nor config file

PanACoTA/utils_argparse.py

@@ -162,7 +162,13 @@ class Conf_all_parser(configparser.ConfigParser):
         self.read(conffile)
         self.sec_dicts = {}
         for sec in sections:
-            self.sec_dicts[sec] = dict(self[sec])
+            # If section in configfile, put its arguments and values to a dict
+            # If not, create empty section, and associate with empty dict
+            if sec in dict(self):
+                self.sec_dicts[sec] = dict(self[sec])
+            else:
+                self.sec_dicts[sec] = {}
+                self.add_section(sec)
 
     def get_section_dict(self, section):
         """
@@ -172,7 +178,8 @@ class Conf_all_parser(configparser.ConfigParser):
 
     def add_default(self, defargs, section):
         """
-        Add all default arguments (defargs) in section dict.
+        Complete 'section' dict with default parameters.
+        If key already defined, keep current value.
         """
         for key, val in defargs.items():
             if key not in self.sec_dicts[section]:
@@ -191,6 +198,7 @@ class Conf_all_parser(configparser.ConfigParser):
     def set_boolean(self, section, param):
         """
         Change param of section to boolean
+        raise error if problem
         """
         try:
             bool_param = self.getboolean(section, param)
@@ -202,7 +210,8 @@ class Conf_all_parser(configparser.ConfigParser):
 
     def set_int(self, section, param):
         """
-        Change param of section to boolean
+        Change param of section to int
+        raise error if problem
         """
         try:
             int_param = self.getint(section, param)
@@ -214,7 +223,8 @@ class Conf_all_parser(configparser.ConfigParser):
 
     def set_float(self, section, param):
         """
-        Change param of section to boolean
+        Change param of section to float
+        raise error if problem
         """
         try:
             float_param = self.getfloat(section, param)