Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/seq/ClusterConsensusCollection.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import re |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 from commons.core.seq.BioseqDB import BioseqDB |
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3 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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 |