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Commit 7338b5c9 authored by Amandine  PERRIN's avatar Amandine PERRIN
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Check parser type from utils_argparse

parent 4b9a2f88
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......@@ -156,28 +156,8 @@ def build_parser(parser):
parser to configure in order to extract command-line arguments
"""
import argparse
import multiprocessing
from PanACoTA import utils_argparse
def thread_num(param):
try:
param = int(param)
except Exception:
msg = "argument --threads threads: invalid int value: {}".format(param)
raise argparse.ArgumentTypeError(msg)
nb_cpu = multiprocessing.cpu_count()
if param > nb_cpu:
msg = ("You have {} threads on your computer, you cannot ask for more: "
"invalid value: {}").format(nb_cpu, param)
raise argparse.ArgumentTypeError(msg)
elif param < 0:
msg = ("Please provide a positive number of threads (or 0 for all threads): "
"Invalid value: {}").format(param)
raise argparse.ArgumentTypeError(msg)
elif param == 0:
return multiprocessing.cpu_count()
return param
# Create command-line parser for all options and arguments to give
required = parser.add_argument_group('Required arguments')
required.add_argument("-l", dest="lstinfo_file", required=True,
......@@ -218,7 +198,7 @@ def build_parser(parser):
help=("use this option if you want to save the concatenated protein "
"databank in another directory than the one containing all "
"individual protein files ('Proteins' folder)."))
optional.add_argument("--threads", dest="threads", default=1, type=thread_num,
optional.add_argument("--threads", dest="threads", default=1, type=utils_argparse.thread_num,
help=("add this option if you want to parallelize on several threads. "
"Indicate on how many threads you want to parallelize. "
"By default, it uses 1 thread. Put 0 if you want to use "
......
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