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# 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.
import unittest
import struct
import os
import sys
try:
from numpy import array
import numpy.testing
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install NumPy if you want to use Bio.Affy.CelFile")
from Bio.Affy import CelFile
def testRecordV4(record):
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')
class AffyTest(unittest.TestCase):
def setUp(self):
self.affy3 = "Affy/affy_v3_example.CEL"
self.affy4 = "Affy/affy_v4_example.CEL"
self.affy4Bad = "Affy/affy_v4_bad_example.CEL"
with open(self.affy4Bad, "wb") as f:
self.writeExampleV4(f, bad=True)
def tearDown(self):
os.remove(self.affy4Bad)
# tests if the code is backwards compatible
def testAffyStrict(self):
record = CelFile.read("hello")
assert record.DatHeader is None
# tests the old Affymetrix v3 parser
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 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)
# tests the new Affymetrix v4 parser
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)
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 testAffyWrongModeRead(self):
try:
with open(self.affy4, "r") as f:
record = CelFile.read(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)
# Writes a small example Affymetrix V4 CEL File
def writeExampleV4(self, f, bad=False):
preHeaders = {'cellNo': 25,
'columns': 5,
'headerLen': 752,
'magic': 64,
'rows': 5,
'version': 4}
goodH = {u'Axis-invertX': b'0'}
badH = {u'Axis-invertX': b'1'}
headers = {u'Algorithm': b'Percentile',
u'AlgorithmParameters': b'Percentile:75;CellMargin:4;Outlie'
b'rHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize'
b':TRUE;FullFeatureWidth:7;FullFeatureHeight:7;IgnoreOutlie'
b'rsInShiftRows:FALSE;FeatureExtraction:TRUE;PoolWidthExten'
b'stion:1;PoolHeightExtension:1;UseSubgrids:FALSE;Randomize'
b'Pixels:FALSE;ErrorBasis:StdvMean;StdMult:1.000000;NumDATS'
b'ubgrids:169',
u'AxisInvertY': b'0',
u'Cols': b'5',
u'DatHeader': b'[0..65534] 20_10N:CLS=19420RWS=19420XIN=0'
b' YIN=0 VE=30 2.0 05/25/05 23:19:07 50102310 M10 '
b' \x14 \x14 HuEx-1_0-st-v2.1sq \x14 \x14 \x14 \x14 '
b'\x14570 \x14 25540.671875 \x14 3.500000 \x14 0.7000 \x14'
b' 3',
u'GridCornerLL': b'518 18668',
u'GridCornerLR': b'18800 18825',
u'GridCornerUL': b'659 469',
u'GridCornerUR': b'18942 623',
u'OffsetX': b'0',
u'OffsetY': b'0',
u'Rows': b'5',
u'TotalX': b'2560',
u'TotalY': b'2560',
u'swapXY': b'0'}
if not bad:
headers.update(goodH)
else:
headers.update(badH)
prePadding = b"this text doesn't matter and is ignored\x04"
preHeadersOrder = ["magic",
"version",
"columns",
"rows",
"cellNo",
"headerLen"]
headersEncoded = struct.pack('<' + 'i' * len(preHeadersOrder),
*[preHeaders[header] for header in
preHeadersOrder])
def packData(intensity, sdev, pixel):
return struct.pack("< f f h", intensity, sdev, pixel)
f.write(headersEncoded)
for header in headers:
try:
f.write(bytes(header, encoding="utf-8") +
b"=" +
headers[header] +
b"\n")
except TypeError:
f.write(header + b"=" + headers[header] + b"\n")
f.write(prePadding)
f.write(b"\x00" * 15)
for i in range(25):
f.write(packData(float(i), float(-i), 9))
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=0)
unittest.main(testRunner=runner)
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