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1 import re
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2 from commons.core.seq.BioseqDB import BioseqDB
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3
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4 ## Record a collection of bioseqDB representing cluster consensus
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5 #
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6 class ClusterConsensusCollection(object):
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7
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8 ## constructor
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9 #
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10 # @param clusterFileName string name of file containing the cluster of consensus
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11 #
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12 def __init__(self, clusterFileName):
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13 self._clusterFileName = clusterFileName
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14 self._lClusterConsensus = []
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15
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16 def __eq__(self, o):
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17 return self._clusterFileName == o._clusterFileName and self._lClusterConsensus == o._lClusterConsensus
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18
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19 def getLClusterConsensus(self):
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20 return self._lClusterConsensus
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21
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22 def fillCollection(self):
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23 iBioseqDBAllCluster = BioseqDB()
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24 fClusterFile = open(self._clusterFileName, "r")
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25 iBioseqDBAllCluster.read(fClusterFile)
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26 fClusterFile.close()
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27 lHeader = iBioseqDBAllCluster.getHeaderList()
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28 firstHeader = lHeader[0]
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29 previousClusterName, seqHeader = self._getClusterNameAndSeqHeader(firstHeader)
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30 clusterConsensus = BioseqDB()
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31 clusterConsensus.setName(previousClusterName)
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32 self._addBioseqInClusterConsensus(iBioseqDBAllCluster, firstHeader, seqHeader, clusterConsensus)
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33 for header in lHeader[1:]:
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34 clusterName, seqHeader = self._getClusterNameAndSeqHeader(header)
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35 if clusterName != previousClusterName:
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36 self._lClusterConsensus.append(clusterConsensus)
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37 previousClusterName = clusterName
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38 clusterConsensus = BioseqDB()
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39 clusterConsensus.setName(previousClusterName)
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40 self._addBioseqInClusterConsensus(iBioseqDBAllCluster, header, seqHeader, clusterConsensus)
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41 self._lClusterConsensus.append(clusterConsensus)
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42
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43 def _getClusterNameAndSeqHeader(self, header):
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44 m = re.match("(\D*)(\d+)Mb\d+\s.*", header)
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45 clusterNumber = m.group(2)
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46 clusterName = m.group(1) + clusterNumber
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47 lPartsHeaderheader = header.split(" ")
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48 seqHeader = lPartsHeaderheader[1]
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49 return clusterName, seqHeader
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50
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51 def _addBioseqInClusterConsensus(self, iBioseqDBAllCluster, firstHeader, seqHeader, clusterConsensus):
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52 ibioseq = iBioseqDBAllCluster.fetch(firstHeader)
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53 ibioseq.setHeader(seqHeader)
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54 clusterConsensus.add(ibioseq)
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55
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56 def getNumClusterForAConsensus(self, seqName):
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57 nbCluster = 1
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58 for bioseqDB in self._lClusterConsensus:
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59 if seqName in bioseqDB.getHeaderList():
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60 return nbCluster
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61 nbCluster += 1
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62
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63 def getNumConsensusInCluster(self, numCluster):
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64 return self._lClusterConsensus[numCluster - 1].getSize()
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65
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66
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