mirror of
https://github.com/Athemis/pyKinetics.git
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65 lines
1.9 KiB
Python
Executable file
65 lines
1.9 KiB
Python
Executable file
#!/usr/bin/python
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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 main():
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# parse command line arguments
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args = parse_arguments()
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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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print('Path containing input data 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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print('Path for writing results 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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data_files = sorted(input_path.glob('**/*.csv'))
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exp = libkinetics.Experiment(data_files, (10, 25), do_hill)
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exp.plot_data(str(output_path))
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exp.plot_kinetics(str(output_path))
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exp.write_data(str(output_path))
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else:
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raise ValueError('{} is not a directory!'.format(input_path))
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else:
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raise ValueError('{} is not a directory!'.format(output_path))
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if __name__ == "__main__":
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main()
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