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https://github.com/Athemis/pyKinetics.git
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Adding logger
This commit is contained in:
parent
7a943cb945
commit
c90c18ee84
2 changed files with 73 additions and 12 deletions
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@ -1,4 +1,5 @@
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#!/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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@ -31,9 +32,39 @@ def parse_arguments():
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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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@ -41,25 +72,38 @@ def main():
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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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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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print('Path for writing results not found: {}'.format(args.output))
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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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raise ValueError('{} is not a directory!'.format(input_path))
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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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raise ValueError('{} is not a directory!'.format(output_path))
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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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@ -1,4 +1,5 @@
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#!/usr/bin/python
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# -*- coding: utf-8 -*-
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from scipy import stats, optimize
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import numpy as np
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@ -9,6 +10,7 @@ import csv
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class Replicate():
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def __init__(self, x, y, owner):
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self.logger = owner.logger
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self.x = x
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self.y = y
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self.owner = owner
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@ -36,6 +38,7 @@ class Replicate():
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class Measurement():
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def __init__(self, x, y, conc, conc_unit, owner):
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self.logger = owner.logger
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self.concentration = float(conc)
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self.concentration_unit = conc_unit
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self.x = x
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@ -89,7 +92,9 @@ class Measurement():
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class Experiment():
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def __init__(self, data_files, xlim, do_hill=False):
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def __init__(self, data_files, xlim, do_hill=False, logger=None):
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self.logger = logger
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# collction of indepentend measurements
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self.measurements = []
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@ -163,7 +168,11 @@ class Experiment():
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'perr': perr,
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'x': x}
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except:
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print('Calculation of Hill kinetics failed!')
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msg = 'Calculation of Michaelis-Menten kinetics failed!'
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if self.logger:
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self.logger.error('ERROR: {}'.format(msg))
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else:
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print(msg)
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return None
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def do_hill_kinetics(self):
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@ -185,7 +194,11 @@ class Experiment():
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'h': h,
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'x': x}
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except:
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print('Calculation of Hill kinetics failed!')
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msg = 'Calculation of Hill kinetics failed!'
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if self.logger:
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self.logger.error('ERROR: {}'.format(msg))
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else:
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print(msg)
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return None
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def plot_kinetics(self, outpath):
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@ -200,12 +213,16 @@ class Experiment():
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fmt='ok', ms=3, fillstyle='none', label="Data with error")
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if self.mm:
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ax.plot(self.mm['x'],
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(self.mm['vmax']*self.mm['x'])/(self.mm['Km']+self.mm['x']), 'b-', label="Michaelis-Menten")
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y = self.mm_kinetics_function(self.mm['x'],
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self.mm['vmax'],
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self.mm['Km'])
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ax.plot(self.mm['x'], y, 'b-', label="Michaelis-Menten")
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if self.hill:
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ax.plot(self.hill['x'],
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((self.hill['vmax']*(self.hill['x']**self.hill['h'])) /
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(self.hill['Kprime'] + (self.hill['x']**self.hill['h']))), 'g-', label="Hill")
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y = self.hill_kinetics_function(self.hill['x'],
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self.hill['vmax'],
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self.hill['Kprime'],
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self.hill['h'])
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ax.plot(self.hill['x'], y, 'g-', label="Hill")
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ax.legend(loc='best', fancybox=True)
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plt.savefig('{}/kinetics.png'.format(outpath), bbox_inches='tight')
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