# 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 os import struct import unittest try: import numpy.testing from numpy import array 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["filter-wavelength"], 570) self.assertAlmostEqual(record.DatHeader["arc-radius"], 25356.509766) self.assertAlmostEqual(record.DatHeader["laser-spotsize"], 3.5) self.assertAlmostEqual(record.DatHeader["pixel-size"], 1.56) 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 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) 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), ) 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(struct.pack("< f f h", i, -i, 9)) # intensity, sdev, pixel if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)