diff --git a/PanACoTA/subcommands/all_modules.py b/PanACoTA/subcommands/all_modules.py
index 6953dab84b153fcdc01154c01e6871ff1a8e0507..35acb3599c5c244f6122e61ff67459e34f810fdc 100644
--- a/PanACoTA/subcommands/all_modules.py
+++ b/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
diff --git a/PanACoTA/utils_argparse.py b/PanACoTA/utils_argparse.py
index 00556b20530642dfb2f3e8ce7f58297eb8350b05..1d3fb39dc0dfed6ce405d6f4947a85955d1177d0 100644
--- a/PanACoTA/utils_argparse.py
+++ b/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)