Athemis/pyKinetics
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Code Issues Releases Wiki Activity

Reformat code using yapf

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This commit is contained in:
Alexander Minges 2015-08-31 19:10:31 +02:00
parent 781c6ccb55
commit c7a8525410
2 changed files with 22 additions and 22 deletions
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16
analyze-cli.py
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@ -41,6 +41,7 @@ class ExperimentHelper():
Provides plotting and data output functionality for libkinetics.Experiment. Provides plotting and data output functionality for libkinetics.Experiment.
""" """
def __init__(self, experiment, logger): def __init__(self, experiment, logger):
self.exp = experiment self.exp = experiment
self.logger = logger self.logger = logger
@ -118,9 +119,7 @@ class ExperimentHelper():
writer = csv.writer(csvfile, dialect='excel-tab') writer = csv.writer(csvfile, dialect='excel-tab')
writer.writerow(['LINEAR FITS']) writer.writerow(['LINEAR FITS'])
writer.writerow([]) writer.writerow([])
writer.writerow(['concentration', writer.writerow(['concentration', 'avg. slope', 'slope std_err',
'avg. slope',
'slope std_err',
'replicates (slope, intercept and r_squared)']) 'replicates (slope, intercept and r_squared)'])
for m in exp.measurements: for m in exp.measurements:
row = [m.concentration, m.avg_slope, m.avg_slope_err] row = [m.concentration, m.avg_slope, m.avg_slope_err]
@ -135,21 +134,18 @@ class ExperimentHelper():
self.logger.debug(' Writing Michaelis-Menten results.') self.logger.debug(' Writing Michaelis-Menten results.')
writer.writerow(['MICHAELIS-MENTEN KINETICS']) writer.writerow(['MICHAELIS-MENTEN KINETICS'])
writer.writerow(['', 'value', 'std']) writer.writerow(['', 'value', 'std'])
writer.writerow(['vmax', exp.mm['vmax'], writer.writerow(['vmax', exp.mm['vmax'], exp.mm['vmax_err']])
exp.mm['vmax_err']]) writer.writerow(['Kprime', exp.mm['Km'], exp.mm['Km_err']])
writer.writerow(['Kprime', exp.mm['Km'],
exp.mm['Km_err']])
if exp.hill: if exp.hill:
self.logger.debug(' Writing Hill results.') self.logger.debug(' Writing Hill results.')
writer.writerow([]) writer.writerow([])
writer.writerow(['HILL KINETICS']) writer.writerow(['HILL KINETICS'])
writer.writerow(['', 'value', 'std']) writer.writerow(['', 'value', 'std'])
writer.writerow(['vmax', exp.hill['vmax'], writer.writerow(['vmax', exp.hill['vmax'],
exp.hill['vmax_err']]) exp.hill['vmax_err']])
writer.writerow(['Kprime', exp.hill['Kprime'], writer.writerow(['Kprime', exp.hill['Kprime'],
exp.hill['Kprime_err']]) exp.hill['Kprime_err']])
writer.writerow(['h', exp.hill['h'], writer.writerow(['h', exp.hill['h'], exp.hill['h_err']])
exp.hill['h_err']])
def parse_arguments(): def parse_arguments():

28
libkinetics/__init__.py
View file

@ -372,11 +372,13 @@ class Experiment():
self.logger.info(' v_max: {} ± {}'.format(vmax, perr[0])) self.logger.info(' v_max: {} ± {}'.format(vmax, perr[0]))
self.logger.info(' Km: {} ± {}'.format(Km, perr[1])) self.logger.info(' Km: {} ± {}'.format(Km, perr[1]))
return {'vmax': np.float(vmax), return {
'Km': np.float(Km), 'vmax': np.float(vmax),
'vmax_err': np.float(perr[0]), 'Km': np.float(Km),
'Km_err': np.float(perr[1]), 'vmax_err': np.float(perr[0]),
'x': x} 'Km_err': np.float(perr[1]),
'x': x
}
def do_hill_kinetics(self): def do_hill_kinetics(self):
""" """
@ -420,10 +422,12 @@ class Experiment():
self.logger.info(' K_prime: {} ± {}'.format(Kprime, perr[1])) self.logger.info(' K_prime: {} ± {}'.format(Kprime, perr[1]))
self.logger.info(' h: {} ± {}'.format(h, perr[2])) self.logger.info(' h: {} ± {}'.format(h, perr[2]))
return {'vmax': np.float(vmax), return {
'Kprime': np.float(Kprime), 'vmax': np.float(vmax),
'vmax_err': np.float(perr[0]), 'Kprime': np.float(Kprime),
'Kprime_err': np.float(perr[1]), 'vmax_err': np.float(perr[0]),
'h_err': np.float(perr[2]), 'Kprime_err': np.float(perr[1]),
'h': np.float(h), 'h_err': np.float(perr[2]),
'x': x} 'h': np.float(h),
'x': x
}