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Complete rewrite of dataset class, with (all) the necessary updates

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Arnar Flatberg
2006-04-24 09:53:07 +00:00
parent 53d0228074
commit a2e4392a72
9 changed files with 426 additions and 234 deletions
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36
test/system/datasettest.py
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@@ -5,28 +5,30 @@ from dataset import *
from scipy import rand,shape
class DatasetTest(unittest.TestCase):
def setUp(self):
self.dim_0_ids = ['sample_a','sample_b']
self.dim_1_ids = ['gene_a','gene_b','gene_c']
self.dim_labels = ['samples','genes']
self.def_list = [[self.dim_labels[0],self.dim_0_ids],[self.dim_labels[1],self.dim_1_ids]]
dim_0_ids = ('sample_a','sample_b')
dim_1_ids = ('gene_a','gene_b','gene_c')
dim_labels = ('samples','genes')
identifiers= [(dim_labels[0],dim_0_ids),(dim_labels[1],dim_1_ids)]
self.array = rand(2,3)
self.testdata = Dataset(self.array,self.def_list)
self.testdata = Dataset(self.array,identifiers)
def testCreation(self):
assert self.testdata._data == self.array
assert 'sample_a' in self.testdata.ids['samples'].keys()
assert 'gene_b' in self.testdata.ids['genes'].keys()
data = self.testdata
assert data._array == self.array
assert 'sample_a' in data['samples'].keys()
assert data['samples']['sample_b']==1
assert 'gene_c' in data['genes'].keys()
assert data['genes']['gene_c']==2
def testExtraction(self):
ids = ['gene_a','gene_b']
dim_name = 'genes'
subset = self.testdata.extract_data(ids,dim_name)
assert shape(subset._data) == (2,2)
assert subset.ids[dim_name].keys() == ids
assert subset.ids[dim_name].values() == [0,1]
#def testExtraction(self):
# ids = ['gene_a','gene_b']
# dim_name = 'genes'
# subset = self.testdata.extract_data(ids,dim_name)
# assert shape(subset._data) == (2,2)
# assert subset.ids[dim_name].keys() == ids
# assert subset.ids[dim_name].values() == [0,1]
if __name__ == '__main__':