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Backwards compatibility with version 3 is maintained. Test cases for package Affy are added. Both new and old code is now tested. affy_v4_example.CEL is added. It is artifically generated and small. See also: http://www.affymetrix.com/estore/support/developer/powertools/changelog/gcos-agcc/cel.html.affx Which explains: Version 3 is generated by the MAS software. This was also known as the ASCII version. Version 4 is generated by the GCOS software. This was also known as the binary or XDA version. Command Console version 1 is generated by the Command Console software. This is stored in the Command Console "generic" data file format. (Squashed commit of pull reqesut #1011)
154 lines
6.3 KiB
Python
154 lines
6.3 KiB
Python
import unittest
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from Bio.Affy import CelFile
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import struct
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import os
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try:
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from numpy import array
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import numpy.testing
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except ImportError:
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from Bio import MissingPythonDependencyError
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raise MissingPythonDependencyError(
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"Install NumPy if you want to use Bio.Affy.CelFile")
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class AffyTest(unittest.TestCase):
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def setUp(self):
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self.affy3 = "Affy/affy_v3_example.CEL"
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self.affy4 = "Affy/affy_v4_example.CEL"
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self.affy4Bad = "Affy/affy_v4_bad_example.CEL"
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with open(self.affy4Bad, "wb") as f:
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self.writeExampleV4(f, bad=True)
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def tearDown(self):
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os.remove(self.affy4Bad)
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# tests if the new strict mode complains about passing a non-file
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def testAffyStrict(self):
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with self.assertRaises(IOError):
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record = CelFile.read("hello", strict=True)
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# tests if the new strict mode is backwards compatible
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def testAffyStrict(self):
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record = CelFile.read("hello")
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assert record.DatHeader is None
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# tests the old Affymetrix v3 parser
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def testAffy3(self):
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with open(self.affy3, "r") as f:
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record = CelFile.read(f)
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assert(len(record.DatHeader) > 0)
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assert(record.intensities.shape == (5, 5))
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assert(record.intensities.shape == record.stdevs.shape)
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assert(record.intensities.shape == record.npix.shape)
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assert(record.ncols == 5)
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assert(record.nrows == 5)
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# tests the new Affymetrix v4 parser
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def testAffy4(self):
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with open(self.affy4, "rb") as f:
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record = CelFile.read(f)
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assert(record.intensities.shape == (5, 5))
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assert(record.intensities.shape == record.stdevs.shape)
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assert(record.intensities.shape == record.npix.shape)
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assert(record.ncols == 5)
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assert(record.nrows == 5)
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numpy.testing.assert_allclose(record.intensities,
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[[0., 1., 2., 3., 4.],
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[5., 6., 7., 8., 9.],
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[10., 11., 12., 13., 14.],
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[15., 16., 17., 18., 19.],
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[20., 21., 22., 23., 24.]])
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numpy.testing.assert_allclose(record.stdevs,
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[[0., -1., -2., -3., -4.],
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[-5., -6., -7., -8., -9.],
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[-10., -11., -12., -13., -14.],
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[-15., -16., -17., -18., -19.],
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[-20., -21., -22., -23., -24.]])
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numpy.testing.assert_allclose(record.npix,
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[[9, 9, 9, 9, 9],
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[9, 9, 9, 9, 9],
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[9, 9, 9, 9, 9],
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[9, 9, 9, 9, 9],
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[9, 9, 9, 9, 9]])
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assert(len(record.AlgorithmParameters) == 329)
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assert(len(record.GridCornerUL) == 7)
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assert(record.AlgorithmParameters[-3:] == '169')
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def testAffyBadHeader(self):
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with self.assertRaises(ValueError):
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with open(self.affy4Bad, "rb") as f:
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record = CelFile.read(f)
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# Writes a small example Affymetrix V4 CEL File
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def writeExampleV4(self, f, bad=False):
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preHeaders = {'cellNo': 25,
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'columns': 5,
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'headerLen': 752,
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'magic': 64,
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'rows': 5,
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'version': 4}
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goodH = {u'Axis-invertX': b'0'}
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badH = {u'Axis-invertX': b'1'}
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headers = {u'Algorithm': b'Percentile',
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u'AlgorithmParameters': b'Percentile:75;CellMargin:4;Outlie'
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b'rHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize'
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b':TRUE;FullFeatureWidth:7;FullFeatureHeight:7;IgnoreOutlie'
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b'rsInShiftRows:FALSE;FeatureExtraction:TRUE;PoolWidthExten'
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b'stion:1;PoolHeightExtension:1;UseSubgrids:FALSE;Randomize'
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b'Pixels:FALSE;ErrorBasis:StdvMean;StdMult:1.000000;NumDATS'
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b'ubgrids:169',
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u'AxisInvertY': b'0',
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u'Cols': b'5',
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u'DatHeader': b'[0..65534] 20_10N:CLS=19420RWS=19420XIN=0'
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b' YIN=0 VE=30 2.0 05/25/05 23:19:07 50102310 M10 '
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b' \x14 \x14 HuEx-1_0-st-v2.1sq \x14 \x14 \x14 \x14 '
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b'\x14570 \x14 25540.671875 \x14 3.500000 \x14 0.7000 \x14'
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b' 3',
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u'GridCornerLL': b'518 18668',
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u'GridCornerLR': b'18800 18825',
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u'GridCornerUL': b'659 469',
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u'GridCornerUR': b'18942 623',
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u'OffsetX': b'0',
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u'OffsetY': b'0',
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u'Rows': b'5',
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u'TotalX': b'2560',
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u'TotalY': b'2560',
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u'swapXY': b'0'}
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if not bad:
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headers.update(goodH)
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else:
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headers.update(badH)
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prePadding = b"this text doesn't matter and is ignored\x04"
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preHeadersOrder = ["magic",
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"version",
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"columns",
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"rows",
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"cellNo",
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"headerLen"]
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headersEncoded = struct.pack('<' + 'i' * len(preHeadersOrder),
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*[preHeaders[header] for header in
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preHeadersOrder])
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def packData(intensity, sdev, pixel):
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return struct.pack("< f f h", intensity, sdev, pixel)
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f.write(headersEncoded)
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for header in headers:
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try:
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f.write(bytes(header, encoding="utf-8") +
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b"=" +
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headers[header] +
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b"\n")
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except TypeError:
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f.write(header + b"=" + headers[header] + b"\n")
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f.write(prePadding)
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f.write(b"\x00" * 15)
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for i in range(25):
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f.write(packData(float(i), float(-i), 9))
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=0)
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unittest.main(testRunner=runner)
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