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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 csv
import matplotlib.pyplot as plt
import numpy as np
from pathlib import Path
from colorlog import ColoredFormatter
@ -35,13 +36,15 @@ class ExperimentHelper():
for r in m.replicates:
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'],
r.x,
r.fitresult['intercept'])
ax.plot(r.x, y, 'k-')
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,
m.concentration,
m.concentration_unit),
@ -107,6 +110,7 @@ class ExperimentHelper():
writer.writerow([exp.hill['vmax'], exp.hill['Kprime'],
exp.hill['h']])
def parse_arguments():
parser = argparse.ArgumentParser()
@ -122,6 +126,12 @@ def parse_arguments():
'--hill',
action='store_true',
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',
type=str,
help='directory containing input files in csv format')
@ -181,6 +191,8 @@ def main():
# initialize logger
logger = initialize_logger()
xlim = (args.start, args.end)
if args.hill:
do_hill = args.hill
else:
@ -213,7 +225,7 @@ def main():
msg = '{} including Hill kinetics'.format(msg)
logger.info('{}'.format(msg))
exp = libkinetics.Experiment(data_files,
(10, 25),
xlim,
do_hill=do_hill,
logger=logger,
fit_to_replicates=fit_to_replicates)