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test_gpu_.py
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test_gpu_.py
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import alphapept.performance
import os
from time import time
import wget
from alphapept.settings import load_settings
from alphapept.paths import DEFAULT_SETTINGS_PATH
import alphapept.interface
import sys
import shutil
import logging
import importlib
import alphapept.feature_finding
FILE_DICT = {}
FILE_DICT['thermo_IRT.raw'] = 'https://datashare.biochem.mpg.de/s/GpXsATZtMwgQoQt/download'
FILE_DICT['IRT_fasta.fasta'] = 'https://datashare.biochem.mpg.de/s/p8Qu3KolzbSiCHH/download'
tmp_folder = 'E:/test_temp/'
def delete_folder(dir_name):
if os.path.exists(dir_name):
shutil.rmtree(dir_name)
def create_folder(dir_name):
if not os.path.exists(dir_name):
logging.info(f'Creating dir {dir_name}.')
os.makedirs(dir_name)
def main():
mode = sys.argv[1]
print(f"Testing with mode {mode}")
global alphapept
alphapept.performance.set_compilation_mode(mode)
alphapept.performance.set_worker_count(0)
importlib.reload(alphapept.feature_finding)
delete_folder(tmp_folder)
create_folder(tmp_folder)
for file in FILE_DICT:
target = os.path.join(tmp_folder, file)
if not os.path.isfile(target):
wget.download(FILE_DICT[file], target)
settings = load_settings(DEFAULT_SETTINGS_PATH)
settings['experiment']['file_paths'] = [os.path.join(tmp_folder, 'thermo_IRT.raw')]
settings['experiment']['fasta_paths'] = [os.path.join(tmp_folder, 'IRT_fasta.fasta')]
import alphapept.interface
settings_ = alphapept.interface.import_raw_data(settings)
start = time()
settings_ = alphapept.interface.feature_finding(settings)
end = time()
te = end-start
print(f'Time elapsed {te}')
if __name__ == "__main__":
main()