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cmd_lipidhunter.py
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cmd_lipidhunter.py
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# -*- coding: utf-8 -*-
#
# Copyright (C) 2016-2019 SysMedOs_team @ AG Bioanalytik, University of Leipzig:
# SysMedOs_team: Zhixu Ni, Georgia Angelidou, Mike Lange, Maria Fedorova
# LipidHunter is Dual-licensed
# For academic and non-commercial use: `GPLv2 License` Please read more information by the following link:
# [The GNU General Public License version 2] (https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)
# For commercial use:
# please contact the SysMedOs_team by email.
# Please cite our publication in an appropriate form.
# Ni, Zhixu, Georgia Angelidou, Mike Lange, Ralf Hoffmann, and Maria Fedorova.
# "LipidHunter identifies phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets."
# Analytical Chemistry (2017).
# DOI: 10.1021/acs.analchem.7b01126
#
# For more info please contact:
# Developer Zhixu Ni [email protected]
# Developer Georgia Angelidou [email protected]
import configparser
import getopt
# required to perform multiprocessing
import multiprocessing
import os.path
import sys
from sys import platform
import time
from typing import List
from LibLipidHunter.Hunter_Core import huntlipids
def main(argv: List[str]) -> bool:
"""
To run LipidHunter from command line, please generate one configuration file by GUI mode and use it as a template.
You can load each time one configuration file only.
Args:
argv (str): -i <input LipidHunter configuration file in .txt format>
Returns:
is_successful(bool): Return True if the run finished with no error message
"""
is_successful = False
_cfg_file = ""
cfg_params_dct = {}
i_type_key_lst = [
"ms_th",
"ms2_th",
"hg_th",
"ms_ppm",
"ms2_ppm",
"hg_ppm",
"dda_top",
"sn_ratio",
"core_number",
"max_ram",
"img_dpi",
"ms_max",
]
f_type_key_lst = [
"rt_start",
"rt_end",
"mz_start",
"mz_end",
"pr_window",
"ms2_infopeak_threshold",
"ms2_hginfopeak_threshold",
"score_filter",
"isotope_score_filter",
"rank_score_filter",
]
b_type_key_lst = ["rank_score", "fast_isotope", "tag_all_sn"]
save_img = True
try:
opts, args = getopt.getopt(argv, "hi:o:n", ["infile="])
except getopt.GetoptError:
print(
"Error: cmd_lipidhunter.py -i <input LipidHunter configuration file in .txt format>"
)
return is_successful
for opt, arg in opts:
if opt == "-h":
print(
"python cmd_lipidhunter.py -i <input LipidHunter configuration file in .txt format>"
)
print("Use -n to skip output image generation (not recommended).")
return is_successful
elif opt in ("-i", "--infile"):
_cfg_file = arg
elif opt == "-n":
save_img = False
if isinstance(_cfg_file, str) and len(_cfg_file) > 0:
print("Input LipidHunter configuration file : ", _cfg_file)
if os.path.isfile(_cfg_file):
with open(_cfg_file) as _cfg_obj:
config = configparser.ConfigParser()
try:
config.read_file(_cfg_obj)
except AttributeError: # for python 2.7.14
config.readfp(_cfg_obj)
print("got file", _cfg_file)
if config.has_section("parameters"):
usr_cfg = "parameters"
options = config.options(usr_cfg)
for param in options:
_val = config.get(usr_cfg, param)
if param in i_type_key_lst:
try:
cfg_params_dct[param] = int(_val)
except ValueError:
cfg_params_dct[param] = int(float(_val))
elif param in f_type_key_lst:
cfg_params_dct[param] = float(_val)
elif param in b_type_key_lst:
if _val.lower() == "true":
cfg_params_dct[param] = True
if _val.lower() == "false":
cfg_params_dct[param] = False
else:
cfg_params_dct[param] = _val
print("Load configuration file... Passed ...")
else:
print(
"Error: Load configuration file FAILED !!! Configuration file content error !!!"
)
return is_successful
else:
print("Load configuration file !!! FAILED !!! File do not exist !!!")
return is_successful
else:
print(
"Error: cmd_lipidhunter.py -i <input LipidHunter configuration file in .txt format>"
)
return is_successful
if len(list(cfg_params_dct.keys())) > 0:
start_time_str = time.strftime("%Y-%m-%d_%H-%M-%S", time.localtime())
cfg_params_dct["hunter_start_time"] = start_time_str
output_folder_path = cfg_params_dct["img_output_folder_str"]
if platform == "linux" or platform == "linux2":
l_cwd = os.getcwd()
if output_folder_path.startswith("/"):
os.chdir("/")
if os.path.isdir(output_folder_path):
print("Folder existed...\n", output_folder_path)
folder_abs_path = os.path.abspath(output_folder_path)
print("abs path of folder\n", folder_abs_path)
else:
if os.path.isdir("/" + output_folder_path):
print("Folder existed...\n", output_folder_path)
folder_abs_path = os.path.abspath(output_folder_path)
print("abs path of folder\n", folder_abs_path)
else:
print("No folder...\n", output_folder_path)
os.makedirs(output_folder_path)
print("Folder created... %s" % output_folder_path)
os.chdir(l_cwd)
else:
if os.path.isdir(output_folder_path):
print("Output folder path... %s" % output_folder_path)
else:
try:
os.mkdir(output_folder_path)
print("Output folder created... %s" % output_folder_path)
except IOError:
print("!! Failed to create output folder !!")
print("Start to process... ", start_time_str)
t, log_lst, export_df = huntlipids(
cfg_params_dct, error_lst=[], save_fig=save_img
)
if len(log_lst) > 0:
for err in log_lst:
print("Error:", err)
print("Error: Please check your parameters!!!")
else:
print(t)
print("Run finished!")
is_successful = True
return is_successful
if __name__ == "__main__":
multiprocessing.freeze_support()
main(sys.argv[1:])