Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/Multifasta2SNPFile.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 import os |
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3 import logging |
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4 from commons.core.utils.FileUtils import FileUtils |
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5 from commons.core.seq.BioseqDB import BioseqDB |
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6 from commons.core.seq.Bioseq import Bioseq |
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7 from commons.core.LoggerFactory import LoggerFactory |
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8 |
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9 DNA_ALPHABET_WITH_N_AND_DELS = set (['A','T','G','C','N','-']) |
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10 IUPAC = set(['A','T','G','C','U','R','Y','M','K','W','S','B','D','H','V','N', '-', 'a','t','g','c','u','r','y','m','k','w','s','b','d','h','v','n']) |
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11 |
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12 class Multifasta2SNPFile( object ): |
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13 |
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14 POLYM_TYPE_4_SNP = "SNP" |
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15 POLYM_TYPE_4_INSERTION = "INSERTION" |
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16 POLYM_TYPE_4_DELETION = "DELETION" |
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17 POLYM_DEFAULT_CONFIDENCE_VALUE = "A" |
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18 SNP_LENGTH = 1 |
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19 FLANK_LENGTH = 250 |
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20 |
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21 def __init__(self, taxon, batchName="", geneName=""): |
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22 |
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23 if(batchName): |
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24 self._batchName = batchName |
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25 |
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26 if(geneName): |
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27 self._geneName = geneName |
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28 |
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29 self._taxon = taxon |
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30 self._outSubSNPFileName = "SubSNP.csv" |
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31 self._outAlleleFileName = "Allele.csv" |
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32 self._outIndividualFileName = "Individual.csv" |
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33 self._outSequenceFSAFileName = "Sequences.fsa" |
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34 self._outSequenceCSVFileName = "Sequences.csv" |
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35 self._outBatchFileName = "Batch.txt" |
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36 self._outBatchLineFileName = "BatchLine.csv" |
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37 self._logFileName = "multifasta2SNP.log" |
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38 |
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39 self._lBatchFileResults = [] |
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40 self._lSubSNPFileResults = [] |
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41 self._lRefSequences = [] |
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42 self._lIndividualFileResults = [] |
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43 self._lBatchLineFileResults = [] |
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44 self._dIndividualNumbers4SubSNPResults = {} |
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45 self._dAlleleFileResults = {} |
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46 |
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47 |
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48 self.dcurrentIndel = {} |
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49 self.lIndelsOfTheCurrentLine = [] |
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50 self.lIndelsOverAllLines = [] |
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51 self.dSNPsPositions = {} |
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52 |
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53 self._iCurrentLineNumber = 0 |
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54 self._currentBatchNumber = 1 |
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55 self.currentLineName = "" |
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56 self.currentNucleotide = "" |
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57 self.currentPosition = 0 |
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58 self._sPolymConfidenceValue = Multifasta2SNPFile.POLYM_DEFAULT_CONFIDENCE_VALUE |
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59 self._sPolymType = Multifasta2SNPFile.POLYM_TYPE_4_SNP |
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60 self._iPolymLength = Multifasta2SNPFile.SNP_LENGTH |
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61 self._fileUtils = FileUtils() |
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62 |
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63 if self._fileUtils.isRessourceExists(self._logFileName): |
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64 os.remove(self._logFileName) |
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65 self._logFile = LoggerFactory.createLogger(self._logFileName, logging.INFO, "%(asctime)s %(levelname)s: %(message)s") |
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66 |
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67 def runOneBatch( self, inFileName): |
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68 self._currentFileName = inFileName |
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69 #TODO: methode a virer; n'utiliser au final que runOneBatchWithoutWriting |
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70 self._wrapper = self.createWrapperFromFile(inFileName) |
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71 self._lBatchFileResults = self.completeBatchList() |
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72 self.detectSNPsAndIndels(self._wrapper) |
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73 self._writeAllOutputFiles() |
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74 self._currentBatchNumber += 1 |
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75 |
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76 def runOneBatchWithoutWriting( self, inFileName): |
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77 self.lIndelsOverAllLines = [] |
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78 self._currentFileName = inFileName |
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79 self._wrapper = self.createWrapperFromFile(inFileName) |
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80 self._lBatchFileResults = self.completeBatchList() |
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81 self.detectSNPsAndIndels(self._wrapper) |
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82 self._currentBatchNumber += 1 |
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83 |
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84 |
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85 def _cleanOutputsInTheCurrentDir(self): |
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86 #TODO: create a list of files to be deleted |
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87 FileUtils.removeFilesByPattern("*.csv") |
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88 if (FileUtils.isRessourceExists(self._outBatchFileName)): |
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89 os.remove(self._outBatchFileName) |
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90 if (FileUtils.isRessourceExists(self._outSequenceFSAFileName)): |
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91 os.remove(self._outSequenceFSAFileName) |
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92 |
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93 |
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94 def _createOutputObjectsIteratingOnCurrentDir(self): |
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95 #TODO: gerer les extensions multiples |
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96 extList = [".fasta", ".fsa"] |
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97 for dirname, dirnames, filenames in os.walk("."): |
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98 filenames.sort() |
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99 for filename in filenames: |
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100 if os.path.splitext(filename)[1] in extList: |
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101 self._geneName = os.path.splitext(filename)[0] |
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102 self._batchName = "Batch_" + self._geneName |
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103 self.runOneBatchWithoutWriting(filename) |
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104 |
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105 def runSeveralBatches( self, inputDir): |
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106 #TODO: enlever les chdirs, appeler les fichiers en absolu et modifier les tests en consequences |
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107 os.chdir(inputDir) |
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108 self._cleanOutputsInTheCurrentDir() |
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109 self._createOutputObjectsIteratingOnCurrentDir() |
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110 self._writeAllOutputFiles() |
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111 os.chdir("../") |
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112 |
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113 |
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114 def _treatADeletionClosingWithAnotherBaseThanRefSeq(self, lineName, nucleotide, position): |
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115 if (self.isTheIndelOpen4ThisLine): |
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116 self._closeTheCurrentIndel(lineName, nucleotide, position) |
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117 self._manageSNPs(lineName, nucleotide, position) |
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118 self.addOnePolymorphicPosition(position) |
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119 |
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120 def _treatNucleotideDifferentThanRefSeqCase(self, refSeq, lineName, index, nucleotide, position): |
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121 if (nucleotide == "-" or refSeq[index] == "-"): |
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122 if (self.isTheIndelOpen4ThisLine): |
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123 self._expandTheCurrentIndel(position, nucleotide) |
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124 else: |
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125 self._startAnIndel(position, nucleotide) |
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126 else: |
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127 self._treatADeletionClosingWithAnotherBaseThanRefSeq(lineName, nucleotide, position) |
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128 |
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129 |
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130 def _treatSameNucleotideInOneIndel(self, refSeq, lineName, index, nucleotide, position): |
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131 if (self._sPolymType == Multifasta2SNPFile.POLYM_TYPE_4_DELETION): |
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132 self._closeTheCurrentIndel(lineName, nucleotide, position) |
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133 elif (self._sPolymType == Multifasta2SNPFile.POLYM_TYPE_4_INSERTION): |
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134 if (refSeq[index] == "-"): |
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135 self._expandTheCurrentIndel(position, nucleotide) |
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136 else: |
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137 self._closeTheCurrentIndel(lineName, nucleotide, position) |
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138 |
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139 def detectSNPsAndIndels(self, iRefAndLines): |
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140 refSeq = iRefAndLines.getReferenceSequence() |
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141 refSeqLength = len ( refSeq ) |
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142 self.dSNPsPositions = {} |
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143 |
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144 for iLineBioseq in iRefAndLines.getLinesBioseqInstances(): |
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145 lineSequence = iLineBioseq.sequence |
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146 self.currentLineName = iLineBioseq.header |
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147 self._manageCurrentIndividual(self.currentLineName) |
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148 |
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149 index = 0 |
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150 self.isTheIndelOpen4ThisLine = 0 |
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151 self.lIndelsOfTheCurrentLine = [] |
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152 for nucleotide in lineSequence: |
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153 position = index + 1 |
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154 if (index < refSeqLength) and self._isSNPDetected(refSeq, index, nucleotide): |
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155 self._treatNucleotideDifferentThanRefSeqCase(refSeq, self.currentLineName, index, nucleotide, position) |
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156 elif(index < refSeqLength and self.isTheIndelOpen4ThisLine) : |
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157 self._treatSameNucleotideInOneIndel(refSeq, self.currentLineName, index, nucleotide, position) |
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158 index = index + 1 |
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159 self.currentNucleotide = nucleotide |
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160 self.currentPosition = position |
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161 |
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162 self.lIndelsOverAllLines = self.lIndelsOverAllLines + self.lIndelsOfTheCurrentLine |
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163 |
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164 self._postTraitementDetectSNP(self.currentLineName, self.currentNucleotide, self.currentPosition) |
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165 |
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166 def _manageCurrentIndividual(self, lineName): |
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167 self._lIndividualFileResults = self._completeIndividualListWithCurrentIndividual(self._lIndividualFileResults, lineName) |
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168 self._lBatchLineFileResults = self._completeBatchLineListWithCurrentIndividual(self._lBatchLineFileResults, self._lIndividualFileResults, lineName) |
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169 if not self._dIndividualNumbers4SubSNPResults.__contains__(lineName): |
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170 self._dIndividualNumbers4SubSNPResults[lineName] = len(self._lIndividualFileResults) |
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171 |
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172 |
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173 def _manageLastPositionIndels(self, lineName, nucleotide, position): |
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174 if (self.isTheIndelOpen4ThisLine): |
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175 self._closeTheCurrentIndel(lineName, nucleotide, position) |
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176 self.lIndelsOverAllLines.append(self.lIndelsOfTheCurrentLine.pop()) |
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177 |
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178 def _postTraitementDetectSNP(self, lineName, nucleotide, position): |
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179 self._manageLastPositionIndels(lineName, nucleotide, position) |
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180 |
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181 self._mergeAllelesAndSubSNPsFromOverlappingIndels() |
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182 self._addMissingsAllelesAndSubSNPs() |
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183 |
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184 self._lSubSNPFileResults = self._sortSubSNPResultByBatchPositionAndLineName(self._lSubSNPFileResults) |
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185 |
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186 def _manageSNPs(self, lineName, nucleotide, position): |
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187 self._dAlleleFileResults = self._completeAlleleSetWithCurrentAllele(self._dAlleleFileResults, nucleotide) |
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188 truePosition = self.getUngappedPositionInRefSeq(position) |
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189 subSNPName = self._formatSubSNPName(lineName, truePosition, Multifasta2SNPFile.POLYM_TYPE_4_SNP) |
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190 iAlleleNumber = self._dAlleleFileResults[nucleotide] |
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191 self._sPolymType = Multifasta2SNPFile.POLYM_TYPE_4_SNP |
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192 flank5Prime, flank3Prime = self.getFlanksOfASubSNP(lineName, position, Multifasta2SNPFile.SNP_LENGTH, Multifasta2SNPFile.FLANK_LENGTH) |
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193 dSubSNPResult = {'subSNPName':subSNPName, 'position':truePosition, 'lineName':self._dIndividualNumbers4SubSNPResults[lineName], |
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194 'allele':iAlleleNumber, 'batchNumber': self._currentBatchNumber, 'confidenceValue':self._sPolymConfidenceValue, |
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195 'type':self._sPolymType, 'length': Multifasta2SNPFile.SNP_LENGTH, |
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196 '5flank':flank5Prime, '3flank':flank3Prime} |
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197 if(not self.subSNPExistsInSubSNPList(dSubSNPResult, self._lSubSNPFileResults)): |
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198 self._lSubSNPFileResults.append(dSubSNPResult) |
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199 |
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200 def _startAnIndel(self, position, nucleotide): |
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201 self.dcurrentIndel['start'] = position |
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202 self.dcurrentIndel['end'] = position |
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203 self.sCurrentIndelAllele = nucleotide |
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204 if(nucleotide == "-"): |
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205 self._sPolymType = Multifasta2SNPFile.POLYM_TYPE_4_DELETION |
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206 else: |
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207 self._sPolymType = Multifasta2SNPFile.POLYM_TYPE_4_INSERTION |
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208 self.isTheIndelOpen4ThisLine = 1 |
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209 |
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210 def _expandTheCurrentIndel(self, position, nucleotide): |
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211 self.sCurrentIndelAllele = self.sCurrentIndelAllele + nucleotide |
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212 self.dcurrentIndel['end'] = position |
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213 |
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214 def _closeTheCurrentIndel(self, lineName, nucleotide, position): |
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215 subSNPName = self._formatSubSNPName(lineName, self.dcurrentIndel['start'], self._sPolymType) |
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216 |
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217 dIndel4TheLine = {'name': subSNPName, 'lineName': lineName, 'start': self.dcurrentIndel['start'],'end' :self.dcurrentIndel['end'], |
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218 'allele': self.sCurrentIndelAllele, 'type': self._sPolymType, 'length': self._iPolymLength} |
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219 |
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220 dIndel4TheLine['length'] = self.getAnIndelLength(dIndel4TheLine) |
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221 |
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222 self.lIndelsOfTheCurrentLine.append(dIndel4TheLine) |
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223 |
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224 self.dcurrentIndel.clear() |
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225 self.isTheIndelOpen4ThisLine = 0 |
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226 |
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227 |
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228 def _mergeAllelesAndSubSNPsFromOverlappingIndels(self): |
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229 lIndelList = [] |
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230 for dIndel in self.lIndelsOverAllLines: |
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231 lIndelList = self.clusteriseIndels(dIndel, self.lIndelsOverAllLines) |
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232 |
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233 for dIndel in lIndelList: |
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234 oldAllele = dIndel['allele'] |
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235 start = dIndel['start'] |
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236 stop = dIndel['end'] |
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237 lineName = dIndel['lineName'] |
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238 |
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239 LineBioSeq = self._wrapper._iLinesBioseqDB.fetch(lineName) |
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240 dIndel = self.updateAllele(oldAllele, start, stop, LineBioSeq, dIndel) |
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241 dSubSNPResult = self.createSubSNPFromAMissingPolym(dIndel, lineName) |
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242 if(not self.subSNPExistsInSubSNPList(dSubSNPResult, self._lSubSNPFileResults)): |
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243 self._lSubSNPFileResults.append(dSubSNPResult) |
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244 |
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245 def updateAllele(self, oldAllele, start, stop, LineBioSeq, dIndel): |
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246 #TODO: creer le test |
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247 newAllele = LineBioSeq.subseq(start, stop).sequence |
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248 if newAllele != oldAllele: |
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249 dIndel['allele'] = newAllele |
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250 self._dAlleleFileResults = self._completeAlleleSetWithCurrentAllele(self._dAlleleFileResults, newAllele) |
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251 return dIndel |
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252 |
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253 |
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254 def getFlanksOfASubSNP(self, lineName, subsnpPosition, polymLength, flankLength): |
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255 bioSeqOfTheLine = self._wrapper._iLinesBioseqDB.fetch(lineName) |
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256 flank5Prime = bioSeqOfTheLine.get5PrimeFlank(subsnpPosition, flankLength) |
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257 flank3Prime = bioSeqOfTheLine.get3PrimeFlank(subsnpPosition, flankLength, polymLength) |
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258 |
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259 return flank5Prime, flank3Prime |
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260 |
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261 def createSubSNPFromAMissingPolym(self, dIndel, lineName): |
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262 if(dIndel['type'] == Multifasta2SNPFile.POLYM_TYPE_4_INSERTION): |
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263 start = self.getUngappedPositionInRefSeq(dIndel['start']-1) |
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264 else: |
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265 start = self.getUngappedPositionInRefSeq(dIndel['start']) |
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266 |
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267 subSNPName = self._formatSubSNPName(dIndel['lineName'], start, dIndel['type']) |
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268 |
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269 iAlleleNumber = self._dAlleleFileResults[dIndel['allele']] |
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270 |
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271 iPolymLength = self.getAnIndelLength(dIndel) |
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272 |
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273 flank5Prime, flank3Prime = self.getFlanksOfASubSNP(lineName, dIndel['start'], iPolymLength, Multifasta2SNPFile.FLANK_LENGTH) |
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274 |
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275 dSubSNPResult = {'subSNPName':subSNPName, 'position':start, 'lineName':self._dIndividualNumbers4SubSNPResults[lineName], 'allele':iAlleleNumber, |
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276 'batchNumber': self._currentBatchNumber, 'confidenceValue':self._sPolymConfidenceValue, 'type':dIndel['type'], |
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277 'length': iPolymLength, '5flank':flank5Prime, '3flank':flank3Prime} |
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278 |
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279 return dSubSNPResult |
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280 |
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281 def clusteriseIndels(self, dIndel, lIndelsOverAllLines): |
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282 iIndice = 0 |
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283 for dIndel in lIndelsOverAllLines: |
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284 iIndice2Compare = 0 |
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285 for dIndel2Compare in lIndelsOverAllLines: |
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286 dIndel, dIndel2Compare = self.mergeBoundsForTwoOverlappingIndels(dIndel, dIndel2Compare) |
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287 lIndelsOverAllLines = self.updateBoundsForAnIndelInAnIndelList(lIndelsOverAllLines, dIndel) |
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288 lIndelsOverAllLines = self.updateBoundsForAnIndelInAnIndelList(lIndelsOverAllLines, dIndel2Compare) |
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289 iIndice2Compare = iIndice2Compare + 1 |
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290 iIndice = iIndice + 1 |
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291 |
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292 return lIndelsOverAllLines |
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293 |
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294 def mergeBoundsForTwoOverlappingIndels(self, dIndel1, dIndel2): |
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295 if((dIndel2['start'] <= dIndel1['start']) and (dIndel2['end'] >= dIndel1['start']) or |
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296 (dIndel1['start'] <= dIndel2['start']) and (dIndel1['end'] >= dIndel2['start'])): |
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297 if(dIndel1['start'] <= dIndel2['start']): |
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298 iStart = dIndel1['start'] |
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299 else: |
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300 iStart = dIndel2['start'] |
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301 |
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302 if(dIndel1['end'] >= dIndel2['end']): |
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303 iEnd = dIndel1['end'] |
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304 else: |
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305 iEnd = dIndel2['end'] |
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306 |
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307 dIndel1['start'] = iStart |
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308 dIndel1['end'] = iEnd |
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309 dIndel2['start'] = iStart |
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310 dIndel2['end'] = iEnd |
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311 |
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312 return dIndel1, dIndel2 |
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313 |
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314 def updateBoundsForAnIndelInAnIndelList(self, lIndelsList, dIndelWithNewBounds): |
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315 name = dIndelWithNewBounds['name'] |
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316 dIndelInTheList, iIndice = self.findAnIndelInAListWithHisName(name, lIndelsList) |
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317 lIndelsList.remove(dIndelInTheList) |
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318 lIndelsList.insert(iIndice, dIndelWithNewBounds) |
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319 return lIndelsList |
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320 |
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321 |
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322 def findASubSNPInAListWithHisName(self, name, lSubSNPList): |
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323 dSubSNP2Find = {} |
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324 indice = 0 |
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325 indice2Find = -1 |
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326 for dSubSNP in lSubSNPList: |
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327 if(dSubSNP['subSNPName'] == name): |
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328 dSubSNP2Find = dSubSNP |
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329 indice2Find = indice |
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330 indice = indice + 1 |
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331 |
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332 if dSubSNP2Find == {} or indice2Find == -1: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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333 msg = "trying to find a SubSNP not existing: " + name |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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334 self._logFile.error(msg) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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335 raise Exception ("trying to find a SubSNP not existing: " + name) |
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336 else: |
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337 return dSubSNP2Find, indice2Find |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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338 |
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339 def subSNPExistsInSubSNPList(self, dSubSNP2Find, lSubSNPList): |
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340 flag = 0 |
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341 for dSubSNP in lSubSNPList: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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342 if(dSubSNP2Find['subSNPName'] == dSubSNP['subSNPName']): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
343 flag = 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
344 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
345 if flag == 1: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
346 return True |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
347 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
348 return False |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
349 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
350 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
351 def findAnIndelInAListWithHisName(self, name, lIndelList): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
352 dIndel2Find = {} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
353 indice = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
354 indice2Find = -1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
355 for dIndel in lIndelList: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
356 if(dIndel['name'] == name): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
357 dIndel2Find = dIndel |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
358 indice2Find = indice |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
359 indice = indice + 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
360 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
361 if dIndel2Find == {} or indice2Find == -1: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
362 msg = "trying to find an indel not existing: " + name |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
363 self._logFile.error(msg) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
364 raise Exception (msg) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
365 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
366 return dIndel2Find, indice2Find |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
367 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
368 def _addMissingsAllelesAndSubSNPs(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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369 for dIndel in self.lIndelsOverAllLines: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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370 start = dIndel['start'] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
371 end = dIndel['end'] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
372 type = dIndel['type'] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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373 self.addMissingAllelesAndSubSNPsForOnePolym(start, end, type) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
374 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
375 for position in self.dSNPsPositions: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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376 self.addMissingAllelesAndSubSNPsForOnePolym(position, position, "SNP") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
377 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
378 def addMissingAllelesAndSubSNPsForOnePolym(self, start, end, polymType): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
379 refSeqAllele = self._wrapper._iReferenceBioseq.subseq(start, end).sequence |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
380 BioSeqDb = self._wrapper.getLinesBioseqInstances() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
381 lBioSeqDbAlleles = self.getAllelesOfASubSeq(BioSeqDb, start, end) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
382 for subSequence in lBioSeqDbAlleles: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
383 if(subSequence['allele'] == refSeqAllele): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
384 lineName = subSequence['header'] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
385 dMissingPolym = {'lineName': lineName, 'start': start,'end' :end, |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
386 'allele': subSequence['allele'], 'type':polymType} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
387 self._dAlleleFileResults = self._completeAlleleSetWithCurrentAllele(self._dAlleleFileResults, subSequence['allele']) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
388 dSubSNPResult = self.createSubSNPFromAMissingPolym(dMissingPolym, lineName) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
389 if(not self.subSNPExistsInSubSNPList(dSubSNPResult, self._lSubSNPFileResults)): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
390 self._lSubSNPFileResults.append(dSubSNPResult) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
391 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
392 def addOnePolymorphicPosition(self, position): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
393 if(not self.dSNPsPositions.has_key(position)): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
394 self.dSNPsPositions[position] = 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
395 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
396 def getUngappedPositionInRefSeq(self, position): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
397 if(position ==1): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
398 nbOfGaps = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
399 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
400 seqIn5Prime = self._wrapper._iReferenceBioseq.subseq(1, position-1).sequence |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
401 nbOfGaps = seqIn5Prime.count("-") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
402 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
403 return position - nbOfGaps |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
404 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
405 def getAllelesOfASubSeq(self, BioSeqDb, start, end): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
406 lAlleles = [] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
407 for iBioSeq in BioSeqDb: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
408 dAlleles = {} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
409 dAlleles['header'] = iBioSeq.header |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
410 dAlleles['allele'] = iBioSeq.subseq(start, end).sequence |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
411 lAlleles.append(dAlleles) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
412 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
413 return lAlleles |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
414 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
415 def getAnIndelLength(self, dIndel): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
416 length = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
417 if(dIndel['type'] == Multifasta2SNPFile.POLYM_TYPE_4_DELETION): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
418 length = dIndel['end'] - dIndel['start'] + 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
419 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
420 length = len(dIndel['allele']) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
421 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
422 return length |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
423 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
424 def createWrapperFromFile(self, inFileName): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
425 faF = open(inFileName, "r") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
426 iBioSeqDB = self._extractSequencesFromInputFile(faF) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
427 faF.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
428 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
429 iBioSeqDB.upCase() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
430 referenceBioseq = iBioSeqDB[0] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
431 linesBioSeqDB = iBioSeqDB.extractPart(1, iBioSeqDB.getSize() - 1) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
432 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
433 try: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
434 if(FileUtils.isEmpty(inFileName)): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
435 msg = "The input file is empty!" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
436 self._logFile.error(self._prefixeWithLineNumber (msg)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
437 raise Exception (self._prefixeWithFileName (msg)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
438 if(self.isHeaderInRefSeqList(referenceBioseq.header)): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
439 msg = "This reference sequence already exists in one previous file!" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
440 self._logFile.error(self._prefixeWithLineNumber (msg)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
441 raise Exception (self._prefixeWithLineNumber (msg)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
442 except Exception, e : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
443 raise Exception ("Problem with one input file: \n" + str(e)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
444 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
445 self._lRefSequences.append(referenceBioseq) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
446 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
447 return ReferenceBioseqAndLinesBioseqDBWrapper(referenceBioseq, linesBioSeqDB, self._logFile, inFileName) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
448 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
449 def isHeaderInRefSeqList(self, header): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
450 isHeader = False |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
451 for item in self._lRefSequences: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
452 if item.header == header: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
453 isHeader = True |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
454 return isHeader |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
455 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
456 def completeBatchList(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
457 dBatchResults = {'BatchNumber' : self._currentBatchNumber, 'BatchName' : self._batchName, 'GeneName' : self._geneName,'ContactNumber' : "1", |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
458 'ProtocolNumber' : "1", 'ThematicNumber' : "1", 'RefSeqName': self._wrapper._iReferenceBioseq.header} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
459 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
460 self._lBatchFileResults.append(dBatchResults) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
461 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
462 return self._lBatchFileResults |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
463 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
464 def getLineAsAHeader(self, lineToBeCheck, lineNumber = 0): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
465 """ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
466 header line begin with the tag(or token) '>' tag |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
467 ended with an carriage return |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
468 contain The name of sequence must respect this alphabet [a-zA-Z0-9_-:] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
469 """ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
470 obsHeader = lineToBeCheck |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
471 if obsHeader[0]!=">" : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
472 msg = "tag '>' omitted before header" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
473 self._logFile.error(self._prefixeWithLineNumber (msg)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
474 raise Exception (self._prefixeWithLineNumber (msg)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
475 else : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
476 obsHeader = obsHeader[1:] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
477 obsHeader = obsHeader.replace ("\n","") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
478 obsHeader = self._removeRepeatedBlanksInAStr(obsHeader) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
479 obsHeader = self._replaceBlankByUnderScoreInAStr(obsHeader) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
480 if self.checkHeaderAlphabet(obsHeader) : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
481 return obsHeader |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
482 self._logFile.error(self._prefixeWithLineNumber ("fatal error on header")) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
483 raise Exception (self._prefixeWithLineNumber ("fatal error on header")) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
484 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
485 def getLineAsASeq(self, lineToBeCheck): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
486 """ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
487 Sequence line |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
488 ended with an carriage return |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
489 contain only character of the IUPAC alphabet |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
490 """ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
491 obsSeq = str.upper(lineToBeCheck) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
492 obsSeq = obsSeq.replace ("\n","") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
493 obsSeq = obsSeq.replace ("\r","") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
494 obsLine = obsSeq.replace("-","") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
495 if not self.isIUPAC_bases(obsLine) : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
496 msg = "the sequence contain a non nucleic character " |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
497 self._logFile.error(self._prefixeWithLineNumber (msg)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
498 raise Exception (self._prefixeWithLineNumber (msg)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
499 return obsSeq |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
500 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
501 def checkHeaderAlphabet( self, strToCheck): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
502 """ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
503 Check the string |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
504 the string is not a header when founding a pattern not corresponding to the regexp |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
505 \W Matches any non-alphanumeric character; this is equivalent to the class [^a-zA-Z0-9_-:]. |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
506 """ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
507 if strToCheck=="": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
508 return False |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
509 p = re.compile('[^a-zA-Z0-9_:\-]', re.IGNORECASE) #p = re.compile('(\W|-|:)+', re.IGNORECASE) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
510 errList=p.findall(strToCheck) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
511 if len( errList ) > 0 : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
512 return False |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
513 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
514 return True |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
515 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
516 ## Check the string is nucleotides sequence from the DNA_ALPHABET_WITH_N = ["A","T","G","C","N"] of IUPAC nomenclature. |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
517 # @return True if sequence contain A, T, G, C or N False otherwise |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
518 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
519 def isDNA_bases( self, sequence): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
520 if sequence == "" : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
521 return False |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
522 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
523 setFromString = set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
524 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
525 for nt in sequence : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
526 setFromString.add(nt) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
527 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
528 return setFromString.issubset(DNA_ALPHABET_WITH_N_AND_DELS) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
529 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
530 ## Check if the string is nucleotides sequence from the IUPAC ALPHABET . |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
531 # @return True if sequence contain IUPAC letters False otherwise |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
532 # |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
533 def isIUPAC_bases( self, sequence): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
534 if sequence == "" : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
535 return False |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
536 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
537 setFromString = set() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
538 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
539 for nt in sequence : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
540 setFromString.add(nt) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
541 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
542 return setFromString.issubset(IUPAC) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
543 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
544 def _writeAllOutputFiles(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
545 writer = Multifasta2SNPFileWriter() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
546 writer.write(self) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
547 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
548 def _sortSubSNPResultByBatchPositionAndLineName(self, lSubSNPResults): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
549 return sorted(lSubSNPResults, key=lambda SNPresults: (SNPresults['batchNumber'], SNPresults['position'], SNPresults['lineName'])) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
550 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
551 def _formatSubSNPName(self, currentLineHeader, position, polymType): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
552 shortPolymType = polymType[:3] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
553 return self._batchName + "_" + shortPolymType + "_" + str(position) + "_" + currentLineHeader |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
554 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
555 def _isSNPDetected(self, referenceSequence, index, nt): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
556 if((nt != referenceSequence[index]) and (nt.upper() != "N") and (referenceSequence[index].upper() != "N")): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
557 return True |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
558 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
559 return False |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
560 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
561 def _extractSequencesFromInputFile(self, inFile): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
562 # attention : DNA_ALPHABET_WITH_N_AND_DELS = Set (['A','T','G','C','N']) no including "gap" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
563 lInFileLines = inFile.readlines() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
564 nbOfLines = len(lInFileLines) - 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
565 #premiere lecture |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
566 self._iCurrentLineNumber = 0 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
567 isSameSeq = False |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
568 newSeq = "" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
569 bioseqDB = BioseqDB () |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
570 while self._iCurrentLineNumber < nbOfLines : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
571 bioseq = Bioseq() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
572 bioseq.header = self.getLineAsAHeader( lInFileLines[self._iCurrentLineNumber] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
573 isSameSeq = True |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
574 while isSameSeq and (self._iCurrentLineNumber < nbOfLines) : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
575 self._iCurrentLineNumber +=1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
576 if lInFileLines[self._iCurrentLineNumber][0] == ">" : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
577 isSameSeq = False |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
578 else : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
579 newSeq = newSeq + self.getLineAsASeq( lInFileLines[self._iCurrentLineNumber] ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
580 isSameSeq = True |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
581 bioseq.setSequence(newSeq) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
582 newSeq = "" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
583 bioseqDB.add(bioseq) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
584 return bioseqDB |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
585 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
586 def _removeRepeatedBlanksInAStr (self, StrToClean ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
587 resStr=StrToClean.expandtabs(2) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
588 compResStr=resStr.replace (" "," ") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
589 while compResStr != resStr : |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
590 resStr=compResStr |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
591 compResStr=resStr.replace (" "," ") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
592 return resStr |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
593 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
594 def _replaceBlankByUnderScoreInAStr (self, StrToClean ): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
595 resStr = StrToClean.replace (" ","_") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
596 return resStr |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
597 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
598 def _prefixeWithLineNumber (self, strMsg): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
599 resStr = "File: " + self._currentFileName + "\t" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
600 resStr += "Line %i " % (self._iCurrentLineNumber+1 ) + strMsg |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
601 return resStr |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
602 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
603 def _prefixeWithFileName (self, strMsg): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
604 resStr = "File: " + self._currentFileName + "\n" + strMsg |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
605 return resStr |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
606 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
607 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
608 def _completeAlleleSetWithCurrentAllele(self, dAlleleFileResults, dnaBase): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
609 if dAlleleFileResults.has_key(dnaBase): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
610 return dAlleleFileResults |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
611 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
612 iAlleleNumber = len(dAlleleFileResults) + 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
613 dAlleleFileResults[dnaBase] = iAlleleNumber |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
614 return dAlleleFileResults |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
615 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
616 def _completeIndividualListWithCurrentIndividual(self, lIndividualResults, lineName): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
617 if lIndividualResults == []: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
618 iIndividualNumber = 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
619 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
620 iIndividualNumber = len(lIndividualResults) + 1 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
621 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
622 #TODO: transformer la liste de dictionnaire en liste d'objets |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
623 if not (self._checkIfALineExistInList(lIndividualResults, lineName)): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
624 dIndividual2Add = {'individualNumber': iIndividualNumber, 'individualName': lineName, 'scientificName': self._taxon} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
625 lIndividualResults.append(dIndividual2Add) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
626 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
627 return lIndividualResults |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
628 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
629 def _completeBatchLineListWithCurrentIndividual(self, lBatchLineResults, lIndividualResults, lineName): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
630 lineDict = self._getALineDictFromADictListWithALineName(lIndividualResults, lineName) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
631 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
632 if len(lineDict) != 0: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
633 if(lineDict.has_key('individualNumber')): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
634 indivNumberOfTheLineDict = lineDict['individualNumber'] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
635 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
636 msg = "Problem with the batchLine results construction: individual named " + lineName + " has no individual number!" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
637 self._logFile.error(msg) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
638 raise Exception (msg) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
639 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
640 msg = "Problem with the batchLine results construction: individual named " + lineName + " not in individual list!" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
641 self._logFile.error(msg) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
642 raise Exception (msg) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
643 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
644 dResults2Add = {'IndividualNumber': str(indivNumberOfTheLineDict), 'BatchNumber' : self._currentBatchNumber} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
645 lBatchLineResults.append(dResults2Add) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
646 return lBatchLineResults |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
647 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
648 def _getALineDictFromADictListWithALineName(self, lDictList, lineName): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
649 dictToReturn = {} |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
650 for myDict in lDictList: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
651 if myDict['individualName'] == lineName: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
652 dictToReturn = myDict |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
653 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
654 return dictToReturn |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
655 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
656 def _checkIfALineExistInList(self, lDictList, lineName): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
657 for myDict in lDictList: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
658 if myDict['individualName'] == lineName: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
659 return True |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
660 return False |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
661 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
662 def _getCurrentBatchResult(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
663 return self._lBatchFileResults[self._currentBatchNumber-1] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
664 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
665 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
666 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
667 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
668 class ReferenceBioseqAndLinesBioseqDBWrapper (object): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
669 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
670 def __init__ (self, iReferenceBioseq, iLinesBioSeqDB, logger, fileName): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
671 self._iReferenceBioseq = iReferenceBioseq |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
672 self._iLinesBioseqDB = iLinesBioSeqDB |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
673 self._logger = logger |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
674 self._currentFileName = fileName |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
675 self._checkAllSeqs() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
676 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
677 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
678 def _checkAllSeqs(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
679 self._iReferenceBioseq.checkEOF() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
680 refSeqLen = self._iReferenceBioseq.getLength() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
681 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
682 for seq in self._iLinesBioseqDB.db: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
683 seq.checkEOF() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
684 if(not seq.getLength() == refSeqLen): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
685 msg = "File: " + self._currentFileName + ", problem with the sequence " + seq.header + ": its length is different from the reference seq! All the sequences must have the same length.\n" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
686 msg += "refseq length: " + str(refSeqLen) + "\n" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
687 msg += "seq length: " + str(seq.getLength()) + "\n" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
688 self._logger.error(msg) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
689 raise Exception (msg) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
690 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
691 def getLinesBioseqInstances(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
692 return self._iLinesBioseqDB.db |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
693 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
694 def getReferenceSequence(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
695 return self._iReferenceBioseq.sequence |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
696 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
697 class Multifasta2SNPFileWriter(object): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
698 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
699 SUB_SNP_FILE_HEADER = ["SubSNPName","ConfidenceValue","Type","Position","5flank", |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
700 "3flank","Length","BatchNumber","IndividualNumber","PrimerType","PrimerNumber","Forward_or_Reverse","AlleleNumber"] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
701 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
702 ALLELE_FILE_HEADER = ["AlleleNumber","Value","Motif","NbCopy","Comment"] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
703 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
704 INDIVIDUAL_FILE_HEADER = ["IndividualNumber","IndividualName","Description","AberrAneuploide", |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
705 "FractionLength","DeletionLineSynthesis","UrlEarImage","TypeLine","ChromNumber","ArmChrom","DeletionBin","ScientificName", |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
706 "local_germplasm_name","submitter_code","local_institute","donor_institute","donor_acc_id"] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
707 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
708 SEQUENCE_CSV_FILE_HEADER = ["SequenceName","SeqType","BankName","BankVersion","ACNumber","Locus","ScientificName"] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
709 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
710 BATCH_TXT_FILE_HEADER = ["BatchNumber", "BatchName", "GeneName", "Description", "ContactNumber", "ProtocolNumber", "ThematicNumber", "RefSeqName", "AlignmentFileName", "SeqName"] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
711 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
712 BATCH_LINE_FILE_HEADER = ["IndividualNumber", "Pos5", "Pos3", "BatchNumber", "Sequence"] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
713 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
714 def __init__(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
715 self._csvFieldSeparator = ";" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
716 self._txtSubFieldSeparator = ": " |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
717 self._txtFieldSeparator = "\n" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
718 self._primerType = "Sequence" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
719 self._csvLineSeparator = "\n" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
720 self._txtLineSeparator = "//\n" |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
721 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
722 def write(self, iMultifasta2SNPFile): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
723 self._writeSubSNPFile(iMultifasta2SNPFile._outSubSNPFileName, iMultifasta2SNPFile._lSubSNPFileResults) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
724 self._writeAlleleFile(iMultifasta2SNPFile._outAlleleFileName, iMultifasta2SNPFile._dAlleleFileResults) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
725 self._writeIndividualFile(iMultifasta2SNPFile._outIndividualFileName, iMultifasta2SNPFile._lIndividualFileResults) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
726 self._writeSequenceFiles(iMultifasta2SNPFile._outSequenceFSAFileName, iMultifasta2SNPFile._outSequenceCSVFileName, iMultifasta2SNPFile._lRefSequences, iMultifasta2SNPFile._taxon) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
727 self._writeBatchFile(iMultifasta2SNPFile._outBatchFileName, iMultifasta2SNPFile._lBatchFileResults) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
728 self._writeBatchLineFile(iMultifasta2SNPFile._outBatchLineFileName, iMultifasta2SNPFile._lBatchLineFileResults) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
729 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
730 def sortAlleleResultByAlleleNumber(self, dAlleleFileResults): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
731 return sorted(dAlleleFileResults.items(), key=lambda(k,v):(v,k)) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
732 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
733 def _writeSubSNPFile(self, subSNPFileName, lSNP2Write): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
734 outF = open(subSNPFileName, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
735 self._writeSNPFileHeader(outF) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
736 for dSNP in lSNP2Write: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
737 self._writeSNPFileLine(outF, dSNP) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
738 outF.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
739 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
740 def _writeAlleleFile(self, alleleFileName, dAllele2Write): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
741 outF = open(alleleFileName, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
742 self._writeAlleleFileHeader(outF) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
743 lAlleleSortedResults = self.sortAlleleResultByAlleleNumber(dAllele2Write) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
744 for tAllele in lAlleleSortedResults: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
745 self._writeAlleleFileLine(outF, tAllele[0], tAllele[1]) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
746 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
747 outF.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
748 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
749 def _writeIndividualFile(self, individualFileName, lIndividual2Write): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
750 sorted(lIndividual2Write, key=lambda Individual: (Individual['individualNumber'])) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
751 outF = open(individualFileName, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
752 self._writeIndividualFileHeader(outF) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
753 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
754 for dIndiv in lIndividual2Write: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
755 self._writeIndividualFileLine(outF, dIndiv) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
756 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
757 outF.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
758 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
759 def _writeSequenceFiles(self, sequenceFSAFileName, sequenceCSVFileName, lRefSequences, taxon): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
760 outFSA = open(sequenceFSAFileName, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
761 outCSV = open(sequenceCSVFileName, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
762 self._writeSequenceCSVHeader(outCSV) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
763 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
764 for refSeq in lRefSequences: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
765 refSeq.cleanGap() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
766 self._writeSequenceFSAFile(outFSA, refSeq) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
767 self._writeSequenceCSVLine(outCSV, refSeq, taxon) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
768 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
769 outFSA.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
770 outCSV.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
771 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
772 def _writeSequenceFSAFile(self, outF, refSeq): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
773 outF.write( ">%s\n" % ( refSeq.header ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
774 outF.write( "%s\n" % ( refSeq.sequence[0:refSeq.getLength()] ) ) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
775 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
776 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
777 def _writeBatchFile(self, batchFileName, lBatchResults): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
778 outF = open(batchFileName, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
779 for dBatchResults in lBatchResults: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
780 for head in Multifasta2SNPFileWriter.BATCH_TXT_FILE_HEADER[:]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
781 if dBatchResults.has_key(head): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
782 outF.write(head + self._txtSubFieldSeparator + str(dBatchResults[head]) + self._txtFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
783 else: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
784 outF.write(head + self._txtSubFieldSeparator + self._txtFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
785 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
786 outF.write(self._txtLineSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
787 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
788 outF.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
789 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
790 def _writeBatchLineFile(self, batchLineFileName, lBatchLineResults): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
791 outF = open(batchLineFileName, "w") |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
792 self._writeBatchLineFileHeader(outF) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
793 for dResult in lBatchLineResults: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
794 self._writeBatchLineFileLine(outF, dResult) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
795 outF.close() |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
796 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
797 def _writeSNPFileHeader(self, outF): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
798 for head in Multifasta2SNPFileWriter.SUB_SNP_FILE_HEADER[:-1]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
799 outF.write(head + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
800 outF.write(Multifasta2SNPFileWriter.SUB_SNP_FILE_HEADER[-1] + self._csvLineSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
801 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
802 def _writeAlleleFileHeader(self, outF): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
803 for head in Multifasta2SNPFileWriter.ALLELE_FILE_HEADER[:-1]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
804 outF.write(head + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
805 outF.write(Multifasta2SNPFileWriter.ALLELE_FILE_HEADER[-1] + self._csvLineSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
806 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
807 def _writeIndividualFileHeader(self, outF): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
808 for head in Multifasta2SNPFileWriter.INDIVIDUAL_FILE_HEADER[:-1]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
809 outF.write(head + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
810 outF.write(Multifasta2SNPFileWriter.INDIVIDUAL_FILE_HEADER[-1] + self._csvLineSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
811 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
812 def _writeSequenceCSVHeader(self, outF): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
813 for head in Multifasta2SNPFileWriter.SEQUENCE_CSV_FILE_HEADER[:-1]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
814 outF.write(head + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
815 outF.write(Multifasta2SNPFileWriter.SEQUENCE_CSV_FILE_HEADER[-1] + self._csvLineSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
816 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
817 def _writeBatchLineFileHeader(self, outF): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
818 for head in Multifasta2SNPFileWriter.BATCH_LINE_FILE_HEADER[:-1]: |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
819 outF.write(head + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
820 outF.write(Multifasta2SNPFileWriter.BATCH_LINE_FILE_HEADER[-1] + self._csvLineSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
821 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
822 def _writeSNPFileLine(self, outF, dSNP): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
823 outF.write(dSNP['subSNPName'] + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
824 outF.write(dSNP['confidenceValue'] + self._csvFieldSeparator + dSNP['type'] + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
825 outF.write(str(dSNP['position']) + self._csvFieldSeparator + dSNP['5flank'] + self._csvFieldSeparator + dSNP['3flank'] + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
826 outF.write(str(dSNP['length']) + self._csvFieldSeparator + str(dSNP['batchNumber']) + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
827 outF.write(str(dSNP['lineName']) + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
828 outF.write(self._primerType + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator + str(dSNP['allele']) + self._csvLineSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
829 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
830 def _writeAlleleFileLine(self, outF, sAllele2Write, iAlleleNumber): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
831 outF.write(str(iAlleleNumber) + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
832 outF.write(sAllele2Write + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator + self._csvLineSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
833 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
834 def _writeIndividualFileLine(self, outF, dIndividual): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
835 outF.write(str(dIndividual['individualNumber']) + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
836 outF.write(dIndividual['individualName'] + self._csvFieldSeparator + self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
837 outF.write(dIndividual['scientificName'] + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator+ self._csvFieldSeparator + self._csvFieldSeparator + self._csvLineSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
838 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
839 def _writeSequenceCSVLine(self, outF, refSeq, taxon): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
840 outF.write(refSeq.header + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
841 outF.write("Reference" + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
842 outF.write(taxon + self._csvLineSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
843 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
844 def _writeBatchLineFileLine(self, outF, dResult): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
845 outF.write(str(dResult['IndividualNumber']) + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
846 outF.write(str(dResult['BatchNumber']) + self._csvFieldSeparator + self._csvLineSeparator) |