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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.
"""Tests for Affy module."""
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 None
from Bio.Affy import CelFile
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 the Affymetrix v3 parser
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)
self.assertEqual(record.AlgorithmParameters["FullFeatureWidth"], 7)
self.assertEqual(record.AlgorithmParameters["FullFeatureHeight"], 7)
self.assertEqual(
record.AlgorithmParameters["IgnoreOutliersInShiftRows"], False
)
self.assertEqual(record.AlgorithmParameters["FeatureExtraction"], True)
self.assertEqual(record.AlgorithmParameters["PoolWidthExtenstion"], 2)
self.assertEqual(record.AlgorithmParameters["PoolHeightExtension"], 2)
self.assertEqual(record.AlgorithmParameters["UseSubgrids"], False)
self.assertEqual(record.AlgorithmParameters["RandomizePixels"], False)
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 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 testAffyBadHeader(self):
with self.assertRaises(CelFile.ParserError):
with open(self.affy4Bad, "rb") as f:
record = CelFile.read(f)
def testAffyWrongModeReadV3(self):
with self.assertRaises(ValueError):
with open(self.affy3, "rb") as f:
record = CelFile.read(f, version=3)
def testAffyWrongModeReadV4(self):
with self.assertRaises(ValueError):
with open(self.affy4, "rt") as f:
record = CelFile.read(f, version=4)
# 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 = {"Axis-invertX": b"0"}
badH = {"Axis-invertX": b"1"}
headers = {
"Algorithm": b"Percentile",
"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",
"AxisInvertY": b"0",
"Cols": b"5",
"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",
"GridCornerLL": b"518 18668",
"GridCornerLR": b"18800 18825",
"GridCornerUL": b"659 469",
"GridCornerUR": b"18942 623",
"OffsetX": b"0",
"OffsetY": b"0",
"Rows": b"5",
"TotalX": b"2560",
"TotalY": b"2560",
"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)
|
