Removed unit test for workflows. The only test file in the directory is
for a workflow that is not used.
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1f9a400057
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import unittest
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import sys
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sys.path.append("../..")
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from workflows.affy_workflow import PhenotypeDataset
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class PhenotypeDatasetTest(unittest.TestCase):
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def testEmptyData(self):
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# we have a list of cel-files, but no categories
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cel_data = """\
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CEL
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02-05-33
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03-07-38
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"""
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dataset = PhenotypeDataset(cel_data)
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self.assertEquals(['CEL', 'phenotypes'], dataset.get_dim_names())
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self.assertEquals(['02-05-33', '03-07-38'], dataset.get_identifiers('CEL'))
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self.assertEquals([], dataset.get_identifiers('phenotypes'))
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def testFloatData(self):
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cel_data = """\
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CEL\tage
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02-05-33\t8.5
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03-07-38\t9
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"""
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dataset = PhenotypeDataset(cel_data)
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self.assertEquals(['CEL', 'phenotypes'], dataset.get_dim_names())
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self.assertEquals(['age'], dataset.get_identifiers('phenotypes'))
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self.assertEquals([[8.5],
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[9]], dataset.asarray().tolist())
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def testCategoryData(self):
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"""Categories expand to one numeric column for each category choice."""
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cel_data = """\
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CEL\tsick
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02-05-33\tyes
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03-07-38\tno
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04-93-33\tyes
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08-32-33\tmaybe
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"""
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dataset = PhenotypeDataset(cel_data)
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self.assertEquals(['CEL', 'phenotypes'], dataset.get_dim_names())
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self.assertEquals(['sick-yes', 'sick-no', 'sick-maybe'], dataset.get_identifiers('phenotypes'))
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self.assertEquals([[1, 0, 0],
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[0, 1, 0],
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[1, 0, 0],
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[0, 0, 1]], dataset.asarray().tolist())
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def testMultipleCategoriesAndFloats(self):
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cel_data = """\
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CEL\tsex\tage\tinfected
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02-05-33\tF\t8\tI
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02-05-34\tF\t9\tN
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02-05-35\tM\t8\tI
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"""
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dataset = PhenotypeDataset(cel_data)
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self.assertEquals(['sex-F', 'sex-M', 'age', 'infected-I', 'infected-N'],
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dataset.get_identifiers('phenotypes'))
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self.assertEquals([[1, 0, 8, 1, 0],
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[1, 0, 9, 0, 1],
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[0, 1, 8, 1, 0]], dataset.asarray().tolist())
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def testGetPhenotypeTable(self):
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cel_data = """\
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CEL\tsex\tage\tinfected
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02-05-33\tF\t8\tI
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02-05-34\tF\t9\tN
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02-05-35\tM\t8\tI
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"""
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dataset = PhenotypeDataset(cel_data)
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self.assertEquals([['CEL', 'sex', 'age', 'infected'],
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['02-05-33', 'F', '8', 'I'],
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['02-05-34', 'F', '9', 'N'],
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['02-05-35', 'M', '8', 'I']], dataset.get_phenotype_table())
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# we can also get a sorted list
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new_order = ['02-05-35', '02-05-33', '02-05-34']
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self.assertEquals([['CEL', 'sex', 'age', 'infected'],
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['02-05-35', 'M', '8', 'I'],
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['02-05-33', 'F', '8', 'I'],
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['02-05-34', 'F', '9', 'N']], dataset.get_phenotype_table(new_order))
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def testGetCategories(self):
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cel_data = """\
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CEL\tsex\tage\tinfected
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02-05-33\tF\t8\tI
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02-05-34\tF\t9\tN
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02-05-35\tM\t8\tI
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"""
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dataset = PhenotypeDataset(cel_data)
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self.assertEquals(set(['F', 'M', 'I', 'N']), set(dataset.get_categories()))
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def testGetFactors(self):
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cel_data = """\
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CEL\tsex\tage\tinfected
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02-05-33\tF\t8\tI
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02-05-34\tF\t9\tN
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02-05-35\tM\t8\tI
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"""
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dataset = PhenotypeDataset(cel_data)
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self.assertEquals(set(["sex", "infected"]), dataset.get_factors(["F", "I"]))
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def testGetCategoryVariable(self):
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"""Can get set/unset list for given category."""
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cel_data = """\
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CEL\tsex\tage\tinfected
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02-05-33\tF\t8\tI
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02-05-34\tF\t9\tN
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02-05-35\tM\t8\tI
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"""
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dataset = PhenotypeDataset(cel_data)
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self.assertEquals([1, 1, 0], dataset.get_category_variable("F"))
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self.assertEquals([0, 0, 1], dataset.get_category_variable("M"))
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self.assertEquals([1, 0, 1], dataset.get_category_variable("I"))
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self.assertEquals([0, 1, 0], dataset.get_category_variable("N"))
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if __name__=='__main__':
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unittest.main()
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