Athemis/pyKinetics
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Add std to results.csv

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This commit is contained in:
Alexander Minges 2015-08-27 15:31:08 +02:00
parent df189d08f0
commit d5e66fd4fe
1 changed files with 31 additions and 18 deletions
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49
analyze-cli.py
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@ -45,9 +45,9 @@ class ExperimentHelper():
y = slope * x + intercept y = slope * x + intercept
return y return y
def plot_data(self, exp, outpath): def plot_data(self, outpath):
# iterate over all measurements # iterate over all measurements
for m in exp.measurements: for m in self.exp.measurements:
# plot each measurement # plot each measurement
fig, ax = plt.subplots() fig, ax = plt.subplots()
ax.set_xlabel('Time') ax.set_xlabel('Time')
@ -73,7 +73,8 @@ class ExperimentHelper():
bbox_inches='tight') bbox_inches='tight')
plt.close(fig) plt.close(fig)
def plot_kinetics(self, exp, outpath): def plot_kinetics(self, outpath):
exp = self.exp
fig, ax = plt.subplots() fig, ax = plt.subplots()
ax.set_xlabel('c [mM]') ax.set_xlabel('c [mM]')
ax.set_ylabel('dA/dt [Au/s]') ax.set_ylabel('dA/dt [Au/s]')
@ -100,37 +101,49 @@ class ExperimentHelper():
plt.savefig('{}/kinetics.png'.format(outpath), bbox_inches='tight') plt.savefig('{}/kinetics.png'.format(outpath), bbox_inches='tight')
plt.close(fig) plt.close(fig)
def write_data(self, exp, outpath): def write_data(self, outpath):
exp = self.exp
with open('{}/results.csv'.format(outpath), with open('{}/results.csv'.format(outpath),
'w', 'w',
newline='\n') as csvfile: newline='\n') as csvfile:
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', 'avg. slope',
'slope std_err', 'slope std_err',
'replicates (slope, intercept and r value)']) '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]
for r in m.replicates: for r in m.replicates:
row.append(r.fitresult['slope']) row.append(r.fitresult['slope'])
row.append(r.fitresult['intercept']) row.append(r.fitresult['intercept'])
row.append(r.fitresult['r_value']) row.append(r.fitresult['r_squared'])
writer.writerow(row) writer.writerow(row)
writer.writerow([]) writer.writerow([])
if exp.mm: if exp.mm:
writer.writerow(['# MICHAELIS-MENTEN KINETICS']) self.logger.debug(' Writing Michaelis-Menten results.')
writer.writerow(['# vmax', 'Km']) writer.writerow(['MICHAELIS-MENTEN KINETICS'])
writer.writerow([exp.mm['vmax'], exp.mm['Km']]) writer.writerow(['', 'value', 'std'])
writer.writerow(['vmax', exp.mm['vmax'],
exp.mm['vmax_err']])
writer.writerow(['Kprime', exp.mm['Km'],
exp.mm['Km_err']])
if exp.hill: if exp.hill:
writer.writerow(['# HILL KINETICS']) self.logger.debug(' Writing Hill results.')
writer.writerow(['# vmax', 'Kprime', 'h']) writer.writerow([])
writer.writerow([exp.hill['vmax'], exp.hill['Kprime'], writer.writerow(['HILL KINETICS'])
exp.hill['h']]) writer.writerow(['', 'value', 'std'])
writer.writerow(['vmax', exp.hill['vmax'],
exp.hill['vmax_err']])
writer.writerow(['Kprime', exp.hill['Kprime'],
exp.hill['Kprime_err']])
writer.writerow(['h', exp.hill['h'],
exp.hill['h_err']])
def parse_arguments(): def parse_arguments():
@ -259,11 +272,11 @@ def main():
fit_to_replicates=fit_to_replicates) fit_to_replicates=fit_to_replicates)
ehlp = ExperimentHelper(exp, logger) ehlp = ExperimentHelper(exp, logger)
logger.info('Plotting linear fits') logger.info('Plotting linear fits')
ehlp.plot_data(exp, str(output_path)) ehlp.plot_data(str(output_path))
logger.info('Plotting kinetic fit(s)') logger.info('Plotting kinetic fit(s)')
ehlp.plot_kinetics(exp, str(output_path)) ehlp.plot_kinetics(str(output_path))
logger.info('Writing results to results.csv') logger.info('Writing results to results.csv')
ehlp.write_data(exp, str(output_path)) ehlp.write_data(str(output_path))
logger.info('Finished!') logger.info('Finished!')
else: else:
msg = '{} is not a directory!'.format(input_path) msg = '{} is not a directory!'.format(input_path)