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https://github.com/Athemis/pyKinetics.git
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109 lines
3.4 KiB
Python
Executable file
109 lines
3.4 KiB
Python
Executable file
#!/usr/bin/python
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# -*- coding: utf-8 -*-
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import argparse
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import logging
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import csv
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from pathlib import Path
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import libkinetics
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def parse_arguments():
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parser = argparse.ArgumentParser()
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parser.add_argument('-v',
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'--verbose',
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action='store_true',
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help='increase output verbosity')
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parser.add_argument('-wh',
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'--with_hill',
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action='store_true',
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help='compute additional kinetics using Hill equation')
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parser.add_argument('input',
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type=str,
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help='directory containing input files in csv format')
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parser.add_argument('output',
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type=str,
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help='results will be written to this directory')
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args = parser.parse_args()
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return args
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def initialize_logger():
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"""
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Initialization of logging subsystem. Two logging handlers are brought up:
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'fh' which logs to a log file and 'ch' which logs to standard output.
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:return logger: returns a logger instance
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"""
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logger = logging.getLogger('pyKinetics-cli')
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logger.setLevel(logging.INFO)
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ch = logging.StreamHandler()
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ch.setLevel(logging.INFO)
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logger.addHandler(ch)
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try:
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log_filename = 'pyKinetics-cli.log'
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fh = logging.FileHandler(log_filename, 'w')
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fh.setLevel(logging.INFO)
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logger.addHandler(fh)
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except IOError as error:
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logger.warning('WARNING: Cannot create log file! Run pyKinetics-cli'
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'from a directory to which you have write access.')
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logger.warning(error.msg)
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pass
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return logger
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def main():
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# parse command line arguments
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args = parse_arguments()
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# initialize logger
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logger = initialize_logger()
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if args.with_hill:
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do_hill = args.with_hill
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else:
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do_hill = False
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try:
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input_path = Path(args.input).resolve()
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except FileNotFoundError:
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logger.critical('CRITICAL: Path containing input data '
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'not found: {}'.format(args.input))
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raise
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try:
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output_path = Path(args.output).resolve()
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except FileNotFoundError:
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logger.critical('CRITICAL: Path for writing results '
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'not found: {}'.format(args.output))
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raise
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if output_path.is_dir():
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if input_path.is_dir():
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logger.info('INFO: Collecting data files')
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data_files = sorted(input_path.glob('**/*.csv'))
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msg = 'Calculating kinetics'
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if do_hill:
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msg = '{} including Hill kinetics'.format(msg)
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logger.info('INFO: {}'.format(msg))
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exp = libkinetics.Experiment(data_files, (10, 25), do_hill)
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logger.info('INFO: Plotting linear fits to data and kinetics')
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exp.plot_data(str(output_path))
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exp.plot_kinetics(str(output_path))
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logger.info('INFO: Writing results to results.csv')
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exp.write_data(str(output_path))
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else:
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msg = '{} is not a directory!'.format(input_path)
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logger.critical('CRITICAL: '.format(msg))
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raise ValueError(msg)
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else:
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msg = '{} is not a directory!'.format(output_path)
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logger.critical('CRITICAL: '.format(msg))
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raise ValueError(msg)
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if __name__ == "__main__":
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main()
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