def test_batch_query(self):
'''
test the batch_query module.
'''
cluster_list = []
for patch in self._name_list:
test_patch = Patch(os.path.join(self._dir, patch))
test_patch.scan()
for cluster in test_patch:
cluster_list.append(cluster)
# Test search orded folder scan
choice_dict = OrderedDict([('receptor', ['NMDA', 'AMPA']),
('mutation', ['S219P', 'S200T']),
('composition', ['a1','ab']),
('agonist', ['glycine', 'taurine']),
('concentration', ['100', '0.1'])])
organisation = {keys:{key: [] for key in choice_dict[keys]} for keys in choice_dict}
for index in range(len(self._name_list)):
temp_filepath = self._dir
for key in choice_dict:
choice = random.choice(choice_dict[key])
temp_filepath = os.path.join(temp_filepath, choice)
organisation[key][choice].extend([index]*self.cluster_num)
try:
os.makedirs(temp_filepath)
except FileExistsError:
pass
shutil.copy2(os.path.join(self._dir, self._name_list[index]),
os.path.join(temp_filepath, self._name_list[index]))
test_batch = Batch(folder_list = self._dir)
if len(test_batch.scan_folder()) != len(cluster_list):
print('scan_folder error')
test_cluster_list = test_batch.scan_orded_folder(clear = True,export = True)
copy_organisation = copy.deepcopy(organisation)
for cluster in test_cluster_list:
index = self._name_list.index(cluster.patchname)
for key in organisation:
if not index in organisation[key][getattr(cluster, key)]:
print('scan_orded_folder error')
else:
copy_organisation[key][getattr(cluster, key)].remove(index)
for i in copy_organisation:
for j in copy_organisation[i]:
if copy_organisation[i][j]:
print('scan_orded_folder error')
# Test query
copy_organisation = copy.deepcopy(organisation)
for i in organisation:
for j in organisation[i]:
if organisation[i][j]:
query_list = test_batch.query(**{i: j})
for cluster in query_list:
index = self._name_list.index(cluster.patchname)
try:
copy_organisation[i][j].remove(index)
except ValueError:
print('query error')
for i in copy_organisation:
for j in copy_organisation[i]:
if copy_organisation[i][j]:
print('query error')
"""
import os
import codecs
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
import pandas as pd
from batch_query import Batch
from batch_analysis import BatchAnalysis, PatchExamination
sns.set(color_codes=True)
batch = Batch('./data/')
batch.scan_orded_folder()
concentation_list = ['0.3', '1', '3', '10', '100']
for concentration in concentation_list:
cluster_list = batch.query(mutation = 'S270T', concentration = concentration)
cluster_summary = BatchAnalysis(cluster_list)
summary = cluster_summary.compute_cluster_summary()
np.savetxt(concentration+'.csv', summary,
fmt= ['%s', '%i', '%.2f', '%.2f','%.2f','%i','%.2f','%.2f'],
delimiter = ',')