# 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)