Athemis/pyKinetics
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Make fitting window configurable via cli parameter

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This commit is contained in:
Alexander Minges 2015-08-24 10:25:06 +02:00
parent c8d7b192fa
commit 04dfff04bc
1 changed files with 14 additions and 2 deletions
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16
analyze-cli.py
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@ -5,6 +5,7 @@ import argparse
import logging import logging
import csv import csv
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
import numpy as np
from pathlib import Path from pathlib import Path
from colorlog import ColoredFormatter from colorlog import ColoredFormatter
@ -35,13 +36,15 @@ class ExperimentHelper():
for r in m.replicates: for r in m.replicates:
ax.plot(r.x, r.y, linestyle='None', ax.plot(r.x, r.y, linestyle='None',
marker='o', ms=3, fillstyle='none') marker='o', ms=3, fillstyle='none',
label='replicate #{}'.format(r.num))
y = self.linear_regression_function(r.fitresult['slope'], y = self.linear_regression_function(r.fitresult['slope'],
r.x, r.x,
r.fitresult['intercept']) r.fitresult['intercept'])
ax.plot(r.x, y, 'k-') ax.plot(r.x, y, 'k-')
ax.axvspan(m.xlim[0], m.xlim[1], facecolor='0.8', alpha=0.5) ax.axvspan(m.xlim[0], m.xlim[1], facecolor='0.8', alpha=0.5)
plt.legend(bbox_to_anchor=(1.05, 1), loc=2, borderaxespad=0.)
plt.savefig('{}/fit_{}_{}.png'.format(outpath, plt.savefig('{}/fit_{}_{}.png'.format(outpath,
m.concentration, m.concentration,
m.concentration_unit), m.concentration_unit),
@ -107,6 +110,7 @@ class ExperimentHelper():
writer.writerow([exp.hill['vmax'], exp.hill['Kprime'], writer.writerow([exp.hill['vmax'], exp.hill['Kprime'],
exp.hill['h']]) exp.hill['h']])
def parse_arguments(): def parse_arguments():
parser = argparse.ArgumentParser() parser = argparse.ArgumentParser()
@ -122,6 +126,12 @@ def parse_arguments():
'--hill', '--hill',
action='store_true', action='store_true',
help='compute additional kinetics using Hill equation') help='compute additional kinetics using Hill equation')
parser.add_argument('start',
type=np.float64,
help='start of fitting window')
parser.add_argument('end',
type=np.float64,
help='end of fitting window')
parser.add_argument('input', parser.add_argument('input',
type=str, type=str,
help='directory containing input files in csv format') help='directory containing input files in csv format')
@ -181,6 +191,8 @@ def main():
# initialize logger # initialize logger
logger = initialize_logger() logger = initialize_logger()
xlim = (args.start, args.end)
if args.hill: if args.hill:
do_hill = args.hill do_hill = args.hill
else: else:
@ -213,7 +225,7 @@ def main():
msg = '{} including Hill kinetics'.format(msg) msg = '{} including Hill kinetics'.format(msg)
logger.info('{}'.format(msg)) logger.info('{}'.format(msg))
exp = libkinetics.Experiment(data_files, exp = libkinetics.Experiment(data_files,
(10, 25), xlim,
do_hill=do_hill, do_hill=do_hill,
logger=logger, logger=logger,
fit_to_replicates=fit_to_replicates) fit_to_replicates=fit_to_replicates)