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# Copyright 2014-2016 Marco Galardini. All rights reserved.
# Adapted from test_Mymodule.py by Jeff Chang
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
try:
import numpy
except ImportError:
from Bio import MissingExternalDependencyError
raise MissingExternalDependencyError(
"Install NumPy if you want to use Bio.phenotype.")
import json
import unittest
from Bio._py3k import StringIO
from Bio import BiopythonExperimentalWarning
import warnings
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonExperimentalWarning)
from Bio import phenotype
# Example plate files
SMALL_JSON_PLATE = 'phenotype/SmallPlate.json'
SMALL_JSON_PLATE_2 = 'phenotype/SmallPlate_2.json'
JSON_PLATE = 'phenotype/Plate.json'
JSON_PLATE_2 = 'phenotype/Plate_2.json'
JSON_PLATE_3 = 'phenotype/Plate_3.json'
JSON_BAD = 'phenotype/BadPlate.json'
SMALL_CSV_PLATES = 'phenotype/SmallPlates.csv'
CSV_PLATES = 'phenotype/Plates.csv'
class TestPhenoMicro(unittest.TestCase):
def test_phenotype_IO_errors(self):
'''Test bad arguments to phenotype IO methods'''
self.assertRaises(ValueError, phenotype.read, CSV_PLATES, 'pm-csv')
self.assertRaises(ValueError, phenotype.read, CSV_PLATES, 'pm-json')
self.assertRaises(
ValueError,
phenotype.read,
CSV_PLATES,
'pm-noformat')
self.assertRaises(ValueError, phenotype.read, CSV_PLATES, 'PM-CSV')
self.assertRaises(TypeError, phenotype.read, CSV_PLATES, 1)
self.assertRaises(KeyError, phenotype.read, JSON_BAD, 'pm-json')
def test_phenotype_IO(self):
'''Test basic functionalities of phenotype IO methods'''
p1 = phenotype.read(SMALL_JSON_PLATE, 'pm-json')
p2 = next(phenotype.parse(SMALL_CSV_PLATES, 'pm-csv'))
handle = StringIO()
c = phenotype.write([p1, p2], handle, 'pm-json')
self.assertEqual(c, 2)
handle.flush()
handle.seek(0)
# Now ready to read back from the handle...
try:
records = list(phenotype.parse(handle, 'pm-json'))
except ValueError as e:
# This is BAD. We can't read our own output.
# I want to see the output when called from the test harness,
# run_tests.py (which can be funny about new lines on Windows)
handle.seek(0)
raise ValueError("%s\n\n%s\n\n%s"
% (str(e), repr(handle.read()), repr(records)))
self.assertEqual(p1, records[0])
handle.close()
handle = StringIO()
self.assertRaises(TypeError, phenotype.write, p1, handle, 1)
self.assertRaises(ValueError, phenotype.write, p1, handle, 'PM-JSON')
self.assertRaises(ValueError, phenotype.write, p1, handle, 'pm-csv')
handle.close()
def test_PlateRecord_errors(self):
'''Test bad arguments with PlateRecord objects'''
self.assertRaises(ValueError,
phenotype.phen_micro.PlateRecord, 'test', [1, 2, 3])
self.assertRaises(TypeError,
phenotype.phen_micro.PlateRecord, 'test', 1)
def test_PlateRecord(self):
'''Test basic functionalities of PlateRecord objects'''
with open(SMALL_JSON_PLATE) as handle:
j = json.load(handle)
p = phenotype.phen_micro.PlateRecord(j['csv_data']['Plate Type'])
times = j['measurements']['Hour']
for k in j['measurements']:
if k == 'Hour':
continue
p[k] = phenotype.phen_micro.WellRecord(k,
signals=dict([(times[i], j['measurements'][k][i])
for i in range(len(times))]))
del j['measurements']
p.qualifiers = j
self.assertEqual(p.id, 'PM01')
self.assertEqual(len(p), 24)
self.assertEqual(p.qualifiers, j)
self.assertRaises(ValueError, p._is_well, 'a')
self.assertEqual(p['A01'].id, 'A01')
self.assertRaises(KeyError, p.__getitem__, 'test')
self.assertEqual(len(p[1]), 12)
self.assertEqual(len(p[1:2:2]), 12)
self.assertEqual(p[1, 2], p['B03'])
self.assertEqual(len(p[:, 1]), 2)
self.assertEqual(len(p[:, 1:4:2]), 4)
self.assertRaises(TypeError, p.__getitem__, 1, 2, 3)
self.assertRaises(IndexError, p.__getitem__, 13)
self.assertRaises(ValueError, p.__setitem__, 'A02', p['A01'])
self.assertRaises(ValueError, p.__setitem__, 'A02', 'a')
p['A02'] = p['A02']
for w in p:
pass
self.assertEqual('A01' in p, True)
self.assertEqual('test' in p, False)
self.assertRaises(ValueError, next, p.get_row('test'))
self.assertEqual(next(p.get_row('A')), p['A01'])
self.assertRaises(ValueError, next, p.get_column('test'))
self.assertEqual(next(p.get_column('12')), p['A12'])
self.assertEqual(next(p.get_column('1')), p['A01'])
self.assertRaises(ValueError, p.subtract_control, 'A121')
self.assertRaises(ValueError, p.subtract_control, wells=['A121'])
p2 = p.subtract_control()
self.assertEqual(p2.id, p.id)
self.assertEqual(p2['A02'], p['A02'] - p['A01'])
self.assertEqual(repr(p), "PlateRecord('WellRecord['A01'], WellRecord" +
"['A02'], WellRecord['A03'], ..., WellRecord['B12']')")
self.assertEqual(str(p), "Plate ID: PM01\nWell: 24\nRows: 2\nColumns: " +
"12\nPlateRecord('WellRecord['A01'], WellRecord['A02'], WellRecord" +
"['A03'], ..., WellRecord['B12']')")
with open(SMALL_JSON_PLATE_2) as handle:
j = json.load(handle)
p1 = phenotype.phen_micro.PlateRecord(j['csv_data']['Plate Type'])
times = j['measurements']['Hour']
for k in j['measurements']:
if k == 'Hour':
continue
p1[k] = phenotype.phen_micro.WellRecord(k,
signals=dict([(times[i], j['measurements'][k][i])
for i in range(len(times))]))
del j['measurements']
p1.qualifiers = j
self.assertRaises(TypeError, p.__add__, 'a')
self.assertRaises(TypeError, p.__sub__, 'a')
p3 = p + p1
self.assertEqual(p3['A02'], p['A02'] + p1['A02'])
p3 = p - p1
self.assertEqual(p3['A02'], p['A02'] - p1['A02'])
del p['A02']
self.assertRaises(ValueError, p.__add__, p1)
self.assertRaises(ValueError, p.__sub__, p1)
def test_bad_fit_args(self):
"""Test error handling of the fit method."""
with open(JSON_PLATE) as handle:
p = json.load(handle)
times = p['measurements']['Hour']
w = phenotype.phen_micro.WellRecord('A10',
signals=dict([(times[i], p['measurements']['A10'][i])
for i in range(len(times))]))
self.assertRaises(ValueError, w.fit, "wibble")
self.assertRaises(ValueError, w.fit, ["wibble"])
self.assertRaises(ValueError, w.fit, ("logistic", "wibble"))
self.assertRaises(ValueError, w.fit, ("wibble", "logistic"))
self.assertRaises(ValueError, w.fit, "logistic") # should be a list/tuple!
def test_WellRecord(self):
'''Test basic functionalities of WellRecord objects'''
with open(JSON_PLATE) as handle:
p = json.load(handle)
times = p['measurements']['Hour']
w = phenotype.phen_micro.WellRecord('A10',
signals=dict([(times[i], p['measurements']['A10'][i])
for i in range(len(times))]))
w1 = phenotype.phen_micro.WellRecord('H12',
signals=dict([(times[i], p['measurements']['H12'][i])
for i in range(len(times))]))
# self.assertIsInstance(w.plate,
# phenotype.phen_micro.PlateRecord)
self.assertTrue(isinstance(w.plate, phenotype.phen_micro.PlateRecord))
self.assertEqual(w.id, 'A10')
self.assertEqual(len(w), len(times))
self.assertEqual(len(w), 384)
self.assertEqual(max(w), (95.75, 217.0))
self.assertEqual(min(w), (0.0, 37.0))
self.assertEqual(max(w, key=lambda x: x[1]),
(16.75, 313.0))
self.assertEqual(min(w, key=lambda x: x[1]),
(0.25, 29.0))
self.assertEqual(len(w[:]), 96)
self.assertEqual(w[1], 29.)
self.assertEqual(w[12], 272.)
self.assertEqual(w[1:5], [29., 35., 39., 43.])
self.assertRaises(ValueError, w.__getitem__, 'a')
self.assertAlmostEqual(w[1:2:.25][0], 29.)
self.assertAlmostEqual(w[1.3567], 33.7196)
self.assertEqual(w.get_raw()[0], (0.0, 37.0))
self.assertEqual(w.get_raw()[-1], (95.75, 217.0))
self.assertEqual(w.get_times()[0], 0.0)
self.assertEqual(w.get_times()[-1], 95.75)
self.assertEqual(w.get_signals()[0], 37.0)
self.assertEqual(w.get_signals()[-1], 217.0)
self.assertEqual(repr(w),
"WellRecord('(0.0, 37.0), (0.25, 29.0), (0.5, 32.0)," +
" (0.75, 30.0), (1.0, 29.0), ..., (95.75, 217.0)')")
self.assertEqual(str(w),
"Well ID: A10\nTime points: 384\nMinum signal 0.25 at " +
"time 29.00\nMaximum signal 16.75 at time " +
"313.00\nWellRecord('(0.0, 37.0), (0.25, 29.0), " +
"(0.5, 32.0), (0.75, 30.0), " +
"(1.0, 29.0), ..., (95.75, 217.0)')")
w.fit(None)
self.assertEqual(w.area, None)
self.assertEqual(w.model, None)
self.assertEqual(w.lag, None)
self.assertEqual(w.plateau, None)
self.assertEqual(w.slope, None)
self.assertEqual(w.v, None)
self.assertEqual(w.y0, None)
self.assertEqual(w.max, 313.0)
self.assertEqual(w.min, 29.0)
self.assertEqual(w.average_height, 217.82552083333334)
self.assertRaises(TypeError, w.__add__, 'a')
w2 = w + w1
self.assertEqual(w2.id, 'A10')
self.assertEqual(len(w2), len(times))
self.assertEqual(len(w2), 384)
self.assertEqual(max(w2), (95.75, 327.0))
self.assertEqual(min(w2), (0.0, 63.0))
self.assertEqual(max(w2, key=lambda x: x[1]),
(18.25, 357.0))
self.assertEqual(min(w2, key=lambda x: x[1]),
(0.25, 55.0))
self.assertEqual(w2[1], 71.)
self.assertEqual(w2[12], 316.)
self.assertEqual(w2[1:5], [71.0, 88.0, 94.0, 94.0])
self.assertAlmostEqual(w2[1:2:.25][0], 71.0)
self.assertAlmostEqual(w2[1.3567], 77.7196)
self.assertEqual(w2.get_raw()[0], (0.0, 63.0))
self.assertEqual(w2.get_raw()[-1], (95.75, 327.0))
self.assertEqual(w2.get_times()[0], 0.0)
self.assertEqual(w2.get_times()[-1], 95.75)
self.assertEqual(w2.get_signals()[0], 63.0)
self.assertEqual(w2.get_signals()[-1], 327.0)
self.assertRaises(TypeError, w.__sub__, 'a')
w2 = w - w1
self.assertEqual(w2.id, 'A10')
self.assertEqual(len(w2), len(times))
self.assertEqual(len(w2), 384)
self.assertEqual(max(w2), (95.75, 107.0))
self.assertEqual(min(w2), (0.0, 11.0))
self.assertEqual(max(w2, key=lambda x: x[1]),
(15.75, 274.0))
self.assertEqual(min(w2, key=lambda x: x[1]),
(3.25, -20.0))
self.assertEqual(w2[1], -13.)
self.assertEqual(w2[12], 228.)
self.assertEqual(w2[1:5], [-13.0, -18.0, -16.0, -8.0])
self.assertAlmostEqual(w2[1:2:.25][0], -13.0)
self.assertAlmostEqual(w2[1.3567], -10.2804)
self.assertEqual(w2.get_raw()[0], (0.0, 11.0))
self.assertEqual(w2.get_raw()[-1], (95.75, 107.0))
self.assertEqual(w2.get_times()[0], 0.0)
self.assertEqual(w2.get_times()[-1], 95.75)
self.assertEqual(w2.get_signals()[0], 11.0)
self.assertEqual(w2.get_signals()[-1], 107.0)
w[1] = 1
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
