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1 import unittest
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2 import os
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3 from commons.core.seq.ClusterConsensusCollection import ClusterConsensusCollection
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4 from commons.core.seq.Bioseq import Bioseq
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5 from commons.core.seq.BioseqDB import BioseqDB
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6
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7 class TestClusterConsensusCollection(unittest.TestCase):
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8
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9 def setUp(self):
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10 self._clusterSequencesFileName = "clusterSequences.fa"
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11 self._ClusterConsensusCollection = ClusterConsensusCollection(self._clusterSequencesFileName)
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12 self._createClusterConsensusFile()
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13
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14 def tearDown(self):
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15 os.remove(self._clusterSequencesFileName)
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16
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17 def test_fillCollection(self):
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18 expClusterConsensusCollection = ClusterConsensusCollection(self._clusterSequencesFileName)
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19 expClusterConsensusCollection._clusterFileName = self._clusterSequencesFileName
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20 bioseq1 = Bioseq("seq1", "ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT")
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21 bioseq2 = Bioseq("seq2", "ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT")
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22 bioseq3 = Bioseq("seq3", "ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT")
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23 iBioseqDB1 = BioseqDB()
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24 iBioseqDB2 = BioseqDB()
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25 iBioseqDB1.setData([bioseq1, bioseq2])
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26 iBioseqDB2.setData([bioseq3])
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27 expClusterConsensusCollection._lClusterConsensus = [iBioseqDB1, iBioseqDB2]
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28 self._ClusterConsensusCollection.fillCollection()
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29 self.assertEqual(expClusterConsensusCollection, self._ClusterConsensusCollection)
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30
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31 def test_getNumClusterForAConsensus_for_seq2(self):
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32 self._ClusterConsensusCollection.fillCollection()
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33 expClusterNumber = 1
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34 obsClusterNumber = self._ClusterConsensusCollection.getNumClusterForAConsensus ("seq2")
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35 self.assertEqual(expClusterNumber, obsClusterNumber)
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36
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37 def test_getNumClusterForAConsensus_for_seq3(self):
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38 self._ClusterConsensusCollection.fillCollection()
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39 expClusterNumber = 2
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40 obsClusterNumber = self._ClusterConsensusCollection.getNumClusterForAConsensus ("seq3")
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41 self.assertEqual(expClusterNumber, obsClusterNumber)
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42
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43 def test_getNumConsensusInCluster_1(self):
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44 self._ClusterConsensusCollection.fillCollection()
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45 expConsensusNumber = 2
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46 obsConsensusNumber = self._ClusterConsensusCollection.getNumConsensusInCluster (1)
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47 self.assertEqual(expConsensusNumber, obsConsensusNumber)
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48
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49 def test_getNumConsensusInCluster_2(self):
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50 self._ClusterConsensusCollection.fillCollection()
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51 expConsensusNumber = 1
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52 obsConsensusNumber = self._ClusterConsensusCollection.getNumConsensusInCluster (2)
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53 self.assertEqual(expConsensusNumber, obsConsensusNumber)
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54
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55 def _createClusterConsensusFile(self):
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56 fCluster = open(self._clusterSequencesFileName, "w")
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57 fCluster.write(">BlastclustCluster1Mb1 seq1\n")
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58 fCluster.write("ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT\n")
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59 fCluster.write(">BlastclustCluster1Mb2 seq2\n")
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60 fCluster.write("ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT\n")
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61 fCluster.write(">BlasterGrouperCluster3Mb1 seq3\n")
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62 fCluster.write("ACCAAAGACACTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACTATTTT\n")
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63 fCluster.close()
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64
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65
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66 if __name__ == "__main__":
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67 unittest.main() |
