def testAffy4(self):
with open(self.affy4, "rb") as f:
record = CelFile.read(f)
self.assertEqual(record.intensities.shape, (5, 5))
self.assertEqual(record.intensities.shape, record.stdevs.shape)
self.assertEqual(record.intensities.shape, record.npix.shape)
self.assertEqual(record.ncols, 5)
self.assertEqual(record.nrows, 5)
global message
try:
numpy.testing.assert_allclose(
record.intensities,
[
[0.0, 1.0, 2.0, 3.0, 4.0],
[5.0, 6.0, 7.0, 8.0, 9.0],
[10.0, 11.0, 12.0, 13.0, 14.0],
[15.0, 16.0, 17.0, 18.0, 19.0],
[20.0, 21.0, 22.0, 23.0, 24.0],
],
)
message = None
except AssertionError as err:
message = str(err)
if message is not None:
self.fail(message)
try:
numpy.testing.assert_allclose(
record.stdevs,
[
[0.0, -1.0, -2.0, -3.0, -4.0],
[-5.0, -6.0, -7.0, -8.0, -9.0],
[-10.0, -11.0, -12.0, -13.0, -14.0],
[-15.0, -16.0, -17.0, -18.0, -19.0],
[-20.0, -21.0, -22.0, -23.0, -24.0],
],
)
message = None
except AssertionError as err:
message = str(err)
if message is not None:
self.fail(message)
try:
numpy.testing.assert_allclose(
record.npix,
[
[9, 9, 9, 9, 9],
[9, 9, 9, 9, 9],
[9, 9, 9, 9, 9],
[9, 9, 9, 9, 9],
[9, 9, 9, 9, 9],
],
)
message = None
except AssertionError as err:
message = str(err)
if message is not None:
self.fail(message)
self.assertEqual(len(record.AlgorithmParameters), 329)
self.assertEqual(len(record.GridCornerUL), 7)
self.assertEqual(record.AlgorithmParameters[-3:], "169")
def testAffy4(self):
with open(self.affy4, "rb") as f:
record = CelFile.read(f)
assert (record.intensities.shape == (5, 5))
assert (record.intensities.shape == record.stdevs.shape)
assert (record.intensities.shape == record.npix.shape)
assert (record.ncols == 5)
assert (record.nrows == 5)
numpy.testing.assert_allclose(
record.intensities,
[[0., 1., 2., 3., 4.], [5., 6., 7., 8., 9.],
[10., 11., 12., 13., 14.], [15., 16., 17., 18., 19.],
[20., 21., 22., 23., 24.]])
numpy.testing.assert_allclose(
record.stdevs,
[[0., -1., -2., -3., -4.], [-5., -6., -7., -8., -9.],
[-10., -11., -12., -13., -14.], [
-15., -16., -17., -18., -19.
], [-20., -21., -22., -23., -24.]])
numpy.testing.assert_allclose(
record.npix,
[[9, 9, 9, 9, 9], [9, 9, 9, 9, 9], [9, 9, 9, 9, 9],
[9, 9, 9, 9, 9], [9, 9, 9, 9, 9]])
assert (len(record.AlgorithmParameters) == 329)
assert (len(record.GridCornerUL) == 7)
assert (record.AlgorithmParameters[-3:] == '169')
def test_read(self):
version = 3
GridCornerUL = (206, 129)
GridCornerUR = (3570, 107)
GridCornerLR = (3597, 3470)
GridCornerLL = (234, 3492)
DatHeader = '[11..65533] 1g_A9AF:CLS=3684 RWS=3684 XIN=1 YIN=1 VE=30 2.0 08/23/07 11:23:24 50205880 M10 Tgondii_SNP1.1sq 570 25356.509766 3.500000 1.5600 6'
Algorithm = 'Percentile'
AlgorithmParameters = 'Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureHeight:7;IgnoreOutliersInShiftRows:FALSE;FeatureExtraction:TRUE;PoolWidthExtenstion:2;PoolHeightExtension:2;UseSubgrids:FALSE;RandomizePixels:FALSE;ErrorBasis:StdvMean;StdMult:1.000000'
NumberCells = 25
intensities = numpy.array([[234.0, 170.0, 22177.0, 164.0, 22104.0],
[188.0, 188.0, 21871.0, 168.0, 21883.0],
[188.0, 193.0, 21455.0, 198.0, 21300.0],
[188.0, 182.0, 21438.0, 188.0, 20945.0],
[193.0, 20370.0, 174.0, 20605.0, 168.0]])
stdevs = numpy.array([[24.0, 34.5, 2669.0, 19.7, 3661.2],
[29.8, 29.8, 2795.9, 67.9, 2792.4],
[29.8, 88.7, 2976.5, 62.0, 2914.5],
[29.8, 76.2, 2759.5, 49.2, 2762.0],
[38.8, 2611.8, 26.6, 2810.7, 24.1]])
npix = numpy.array([[25, 25, 25, 25, 25], [25, 25, 25, 25, 25],
[25, 25, 25, 25, 25], [25, 25, 25, 25, 25],
[25, 25, 25, 25, 25]])
nrows = 5
ncols = 5
nmask = 3
mask = numpy.array([[0., 0., 0., 0., 0.], [0., 0., 0., 1., 1.],
[0., 0., 0., 0., 1.], [0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.]])
noutliers = 3
outliers = [[0., 0., 0., 0., 0.], [0., 1., 1., 0., 0.],
[0., 0., 0., 0., 0.], [0., 1., 0., 0., 0.],
[0., 0., 0., 0., 0.]]
nmodified = 3
modified = [[0., 0., 0., 0., 0.], [0., 0., 0., 189., 220.],
[0., 0., 0., 21775., 0.], [0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.]]
with open('./Affy/affy_v3_example.CEL') as handle:
cel = CelFile.read(handle)
self.assertEqual(version, cel.version)
self.assertEqual(GridCornerUL, cel.GridCornerUL)
self.assertEqual(GridCornerUR, cel.GridCornerUR)
self.assertEqual(GridCornerLR, cel.GridCornerLR)
self.assertEqual(GridCornerLL, cel.GridCornerLL)
self.assertEqual(DatHeader, cel.DatHeader)
self.assertEqual(Algorithm, cel.Algorithm)
self.assertEqual(AlgorithmParameters, cel.AlgorithmParameters)
self.assertEqual(NumberCells, cel.NumberCells)
assert_array_equal(intensities, cel.intensities)
assert_array_equal(stdevs, cel.stdevs)
assert_array_equal(npix, cel.npix)
self.assertEqual(nrows, cel.nrows)
self.assertEqual(ncols, cel.ncols)
self.assertEqual(nmask, cel.nmask)
assert_array_equal(mask, cel.mask)
self.assertEqual(noutliers, cel.noutliers)
assert_array_equal(outliers, cel.outliers)
self.assertEqual(nmodified, cel.nmodified)
assert_array_equal(modified, cel.modified)
def testAffy4(self):
with open(self.affy4, "rb") as f:
record = CelFile.read(f)
assert(record.intensities.shape == (5, 5))
assert(record.intensities.shape == record.stdevs.shape)
assert(record.intensities.shape == record.npix.shape)
assert(record.ncols == 5)
assert(record.nrows == 5)
numpy.testing.assert_allclose(record.intensities,
[[0., 1., 2., 3., 4.],
[5., 6., 7., 8., 9.],
[10., 11., 12., 13., 14.],
[15., 16., 17., 18., 19.],
[20., 21., 22., 23., 24.]])
numpy.testing.assert_allclose(record.stdevs,
[[0., -1., -2., -3., -4.],
[-5., -6., -7., -8., -9.],
[-10., -11., -12., -13., -14.],
[-15., -16., -17., -18., -19.],
[-20., -21., -22., -23., -24.]])
numpy.testing.assert_allclose(record.npix,
[[9, 9, 9, 9, 9],
[9, 9, 9, 9, 9],
[9, 9, 9, 9, 9],
[9, 9, 9, 9, 9],
[9, 9, 9, 9, 9]])
assert(len(record.AlgorithmParameters) == 329)
assert(len(record.GridCornerUL) == 7)
assert(record.AlgorithmParameters[-3:] == '169')
def testAffy3(self):
with open(self.affy3, "r") as f:
record = CelFile.read(f)
assert(len(record.DatHeader) > 0)
assert(record.intensities.shape == (5, 5))
assert(record.intensities.shape == record.stdevs.shape)
assert(record.intensities.shape == record.npix.shape)
assert(record.ncols == 5)
assert(record.nrows == 5)
def testAffy3(self):
with open(self.affy3, "r") as f:
record = CelFile.read(f)
assert (len(record.DatHeader) > 0)
assert (record.intensities.shape == (5, 5))
assert (record.intensities.shape == record.stdevs.shape)
assert (record.intensities.shape == record.npix.shape)
assert (record.ncols == 5)
assert (record.nrows == 5)
def testAffyWrongModeReadV4(self):
try:
with open(self.affy4, "r") as f:
record = CelFile.read_v4(f)
except CelFile.ParserError:
if int(sys.version[0]) >= 3:
return # As expected in pyhthon 3
else:
raise AssertionError("Expected CelFile.ParserError in python3")
# the code just works in python 2
testRecordV4(record)
def testAffyWrongModeReadV4(self):
try:
with open(self.affy4, "r") as f:
record = CelFile.read_v4(f)
except CelFile.ParserError:
if int(sys.version[0]) >= 3:
return # As expected in pyhthon 3
else:
raise AssertionError("Expected CelFile.ParserError in python3")
# the code just works in python 2
testRecordV4(record)
def testAffy3Backwards(self):
# tests the old Affymetrix v3 parser
with open(self.affy3, "r") as f:
lines = f.readlines()
record = CelFile.read_v3(lines)
assert(len(record.DatHeader) > 0)
assert(record.intensities.shape == (5, 5))
assert(record.intensities.shape == record.stdevs.shape)
assert(record.intensities.shape == record.npix.shape)
assert(record.ncols == 5)
assert(record.nrows == 5)
def testAffy3Backwards(self):
# tests the old Affymetrix v3 parser
with open(self.affy3, "r") as f:
lines = f.readlines()
record = CelFile.read_v3(lines)
assert (len(record.DatHeader) > 0)
assert (record.intensities.shape == (5, 5))
assert (record.intensities.shape == record.stdevs.shape)
assert (record.intensities.shape == record.npix.shape)
assert (record.ncols == 5)
assert (record.nrows == 5)
def testAffyStrict(self):
with self.assertRaises(IOError):
record = CelFile.read("hello", strict=True)
def testAffyBadHeader(self):
with self.assertRaises(CelFile.ParserError):
with open(self.affy4Bad, "rb") as f:
record = CelFile.read(f)
##from Bio.Affy import CelFile
##with open("Affy/affy_v4_example.CEL", "rb") as handle:
## c = CelFile.read(handle)
from Bio.Affy import CelFile
with open("Data/GSE58661_RAW/GSM1416528_LUNG3-01.CEL", "rb") as handle:
c = CelFile.read_v3(handle)
def testAffyStrict(self):
record = CelFile.read("hello")
assert record.DatHeader is None
def testAffy3(self):
with open(self.affy3) as f:
record = CelFile.read(f)
self.assertGreater(len(record.DatHeader), 0)
self.assertEqual(record.intensities.shape, (5, 5))
self.assertEqual(record.intensities.shape, record.stdevs.shape)
self.assertEqual(record.intensities.shape, record.npix.shape)
self.assertEqual(record.ncols, 5)
self.assertEqual(record.nrows, 5)
self.assertEqual(record.version, 3)
self.assertEqual(record.GridCornerUL, (206, 129))
self.assertEqual(record.GridCornerUR, (3570, 107))
self.assertEqual(record.GridCornerLR, (3597, 3470))
self.assertEqual(record.GridCornerLL, (234, 3492))
self.assertEqual(record.DatHeader["filename"], "1g_A9AF")
self.assertEqual(record.DatHeader["CLS"], 3684)
self.assertEqual(record.DatHeader["RWS"], 3684)
self.assertEqual(record.DatHeader["XIN"], 1)
self.assertEqual(record.DatHeader["YIN"], 1)
self.assertEqual(record.DatHeader["VE"], 30)
self.assertAlmostEqual(record.DatHeader["laser-power"], 2.0)
self.assertEqual(record.DatHeader["scan-date"], "08/23/07")
self.assertEqual(record.DatHeader["scan-time"], "11:23:24")
self.assertEqual(record.DatHeader["scanner-id"], "50205880")
self.assertEqual(record.DatHeader["scanner-type"], "M10")
self.assertEqual(record.DatHeader["array-type"],
"Tgondii_SNP1.1sq")
self.assertEqual(record.DatHeader["image-orientation"], 6)
self.assertEqual(record.Algorithm, "Percentile")
self.assertEqual(len(record.AlgorithmParameters), 16)
self.assertEqual(record.AlgorithmParameters["Percentile"], 75)
self.assertEqual(record.AlgorithmParameters["CellMargin"], 2)
self.assertAlmostEqual(record.AlgorithmParameters["OutlierHigh"],
1.500)
self.assertAlmostEqual(record.AlgorithmParameters["OutlierLow"],
1.004)
self.assertEqual(record.AlgorithmParameters["AlgVersion"], "6.0")
self.assertEqual(record.AlgorithmParameters["FixedCellSize"],
True) # noqa: A502
self.assertEqual(record.AlgorithmParameters["FullFeatureWidth"], 7)
self.assertEqual(record.AlgorithmParameters["FullFeatureHeight"],
7)
self.assertEqual(
record.AlgorithmParameters["IgnoreOutliersInShiftRows"],
False) # noqa: A502
self.assertEqual(record.AlgorithmParameters["FeatureExtraction"],
True) # noqa: A502
self.assertEqual(record.AlgorithmParameters["PoolWidthExtenstion"],
2)
self.assertEqual(record.AlgorithmParameters["PoolHeightExtension"],
2)
self.assertEqual(record.AlgorithmParameters["UseSubgrids"],
False) # noqa: A502
self.assertEqual(record.AlgorithmParameters["RandomizePixels"],
False) # noqa: A502
self.assertEqual(record.AlgorithmParameters["ErrorBasis"],
"StdvMean")
self.assertAlmostEqual(record.AlgorithmParameters["StdMult"], 1.0)
self.assertEqual(record.NumberCells, 25)
global message
try:
numpy.testing.assert_allclose(
record.intensities,
[
[234.0, 170.0, 22177.0, 164.0, 22104.0],
[188.0, 188.0, 21871.0, 168.0, 21883.0],
[188.0, 193.0, 21455.0, 198.0, 21300.0],
[188.0, 182.0, 21438.0, 188.0, 20945.0],
[193.0, 20370.0, 174.0, 20605.0, 168.0],
],
)
message = None
except AssertionError as err:
message = str(err)
if message is not None:
self.fail(message)
try:
numpy.testing.assert_allclose(
record.stdevs,
[
[24.0, 34.5, 2669.0, 19.7, 3661.2],
[29.8, 29.8, 2795.9, 67.9, 2792.4],
[29.8, 88.7, 2976.5, 62.0, 2914.5],
[29.8, 76.2, 2759.5, 49.2, 2762.0],
[38.8, 2611.8, 26.6, 2810.7, 24.1],
],
)
message = None
except AssertionError as err:
message = str(err)
if message is not None:
self.fail(message)
try:
numpy.testing.assert_array_equal(
record.npix,
[
[25, 25, 25, 25, 25],
[25, 25, 25, 25, 25],
[25, 25, 25, 25, 25],
[25, 25, 25, 25, 25],
[25, 25, 25, 25, 25],
],
)
message = None
except AssertionError as err:
message = str(err)
if message is not None:
self.fail(message)
self.assertEqual(record.nmask, 3)
try:
numpy.testing.assert_array_equal(
record.mask,
[
[False, False, False, False, False],
[False, False, False, True, True],
[False, False, False, False, True],
[False, False, False, False, False],
[False, False, False, False, False],
],
)
message = None
except AssertionError as err:
message = str(err)
if message is not None:
self.fail(message)
self.assertEqual(record.noutliers, 3)
try:
numpy.testing.assert_array_equal(
record.outliers,
[
[False, False, False, False, False],
[False, True, True, False, False],
[False, False, False, False, False],
[False, True, False, False, False],
[False, False, False, False, False],
],
)
message = None
except AssertionError as err:
message = str(err)
if message is not None:
self.fail(message)
self.assertEqual(record.nmodified, 3)
try:
numpy.testing.assert_allclose(
record.modified,
[
[0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 189.0, 220.0],
[0.0, 0.0, 0.0, 21775.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0],
],
)
message = None
except AssertionError as err:
message = str(err)
if message is not None:
self.fail(message)
def testAffyWrongModeReadV4(self):
with self.assertRaises(ValueError):
with open(self.affy4, "rt") as f:
record = CelFile.read(f, version=4)
def testAffyStrict(self):
record = CelFile.read("hello")
assert record.DatHeader is None
def testAffy4(self):
with open(self.affy4, "rb") as f:
record = CelFile.read(f)
testRecordV4(record)
def testAffy4(self):
with open(self.affy4, "rb") as f:
record = CelFile.read(f)
testRecordV4(record)
def testAffyBadHeader(self):
with self.assertRaises(CelFile.ParserError):
with open(self.affy4Bad, "rb") as f:
record = CelFile.read(f)
maxInt = int(maxInt / 10)
decrement = True
if not os.path.exists('./json_temp'):
os.makedirs('./json_temp')
cel_filenames = ['159834720_B', '597785396_B']
cel_results = {}
for cel_filename in cel_filenames:
try:
cel_results[cel_filename] = json.load(
open('./json_temp/' + cel_filename + '.CEL.json'))
except FileNotFoundError:
with open('./input/' + cel_filename + '.CEL', 'rb') as handle:
c = CelFile.read(handle)
cel_results[cel_filename] = {}
for i in range(c.nrows):
cel_results[cel_filename][i] = {}
for j in range(c.ncols):
cel_results[cel_filename][i][j] = c.intensities[i][j]
with open('./json_temp/' + cel_filename + '.CEL.json',
'w',
encoding='utf-8') as results:
results.write(json.dumps(cel_results[cel_filename]))
try:
cdf_results = json.load(open('./json_temp/HuEx-1_0-st-v2.text.cdf.json'))
except FileNotFoundError:
cdf_results = {}
with open('./input/HuEx-1_0-st-v2.text.cdf', 'r') as file:
def test_read(self):
version = 3
GridCornerUL = (206, 129)
GridCornerUR = (3570, 107)
GridCornerLR = (3597, 3470)
GridCornerLL = (234, 3492)
DatHeader = '[11..65533] 1g_A9AF:CLS=3684 RWS=3684 XIN=1 YIN=1 VE=30 2.0 08/23/07 11:23:24 50205880 M10 Tgondii_SNP1.1sq 570 25356.509766 3.500000 1.5600 6'
Algorithm = 'Percentile'
AlgorithmParameters = 'Percentile:75;CellMargin:2;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureHeight:7;IgnoreOutliersInShiftRows:FALSE;FeatureExtraction:TRUE;PoolWidthExtenstion:2;PoolHeightExtension:2;UseSubgrids:FALSE;RandomizePixels:FALSE;ErrorBasis:StdvMean;StdMult:1.000000'
NumberCells = 25
intensities = numpy.array([[234.0, 170.0, 22177.0, 164.0, 22104.0],
[188.0, 188.0, 21871.0, 168.0, 21883.0],
[188.0, 193.0, 21455.0, 198.0, 21300.0],
[188.0, 182.0, 21438.0, 188.0, 20945.0],
[193.0, 20370.0, 174.0, 20605.0, 168.0]])
stdevs = numpy.array([[24.0, 34.5, 2669.0, 19.7, 3661.2],
[29.8, 29.8, 2795.9, 67.9, 2792.4],
[29.8, 88.7, 2976.5, 62.0, 2914.5],
[29.8, 76.2, 2759.5, 49.2, 2762.0],
[38.8, 2611.8, 26.6, 2810.7, 24.1]])
npix = numpy.array([[25, 25, 25, 25, 25],
[25, 25, 25, 25, 25],
[25, 25, 25, 25, 25],
[25, 25, 25, 25, 25],
[25, 25, 25, 25, 25]])
nrows = 5
ncols = 5
nmask = 3
mask = numpy.array([[0., 0., 0., 0., 0.],
[0., 0., 0., 1., 1.],
[0., 0., 0., 0., 1.],
[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.]])
noutliers = 3
outliers = [[0., 0., 0., 0., 0.],
[0., 1., 1., 0., 0.],
[0., 0., 0., 0., 0.],
[0., 1., 0., 0., 0.],
[0., 0., 0., 0., 0.]]
nmodified = 3
modified = [[0., 0., 0., 0., 0.],
[0., 0., 0., 189., 220.],
[0., 0., 0., 21775., 0.],
[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.]]
with open('./Affy/affy_v3_example.CEL') as handle:
cel = CelFile.read(handle)
self.assertEqual(version, cel.version)
self.assertEqual(GridCornerUL, cel.GridCornerUL)
self.assertEqual(GridCornerUR, cel.GridCornerUR)
self.assertEqual(GridCornerLR, cel.GridCornerLR)
self.assertEqual(GridCornerLL, cel.GridCornerLL)
self.assertEqual(DatHeader, cel.DatHeader)
self.assertEqual(Algorithm, cel.Algorithm)
self.assertEqual(AlgorithmParameters, cel.AlgorithmParameters)
self.assertEqual(NumberCells, cel.NumberCells)
assert_array_equal(intensities, cel.intensities)
assert_array_equal(stdevs, cel.stdevs)
assert_array_equal(npix, cel.npix)
self.assertEqual(nrows, cel.nrows)
self.assertEqual(ncols, cel.ncols)
self.assertEqual(nmask, cel.nmask)
assert_array_equal(mask, cel.mask)
self.assertEqual(noutliers, cel.noutliers)
assert_array_equal(outliers, cel.outliers)
self.assertEqual(nmodified, cel.nmodified)
assert_array_equal(modified, cel.modified)
def testAffyStrict(self):
with self.assertRaises(IOError):
record = CelFile.read("hello", strict=True)
