Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/seq/BioseqDB.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 # Copyright INRA (Institut National de la Recherche Agronomique) |
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2 # http://www.inra.fr |
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3 # http://urgi.versailles.inra.fr |
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4 # |
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5 # This software is governed by the CeCILL license under French law and |
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6 # abiding by the rules of distribution of free software. You can use, |
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7 # modify and/ or redistribute the software under the terms of the CeCILL |
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8 # license as circulated by CEA, CNRS and INRIA at the following URL |
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9 # "http://www.cecill.info". |
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10 # |
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11 # As a counterpart to the access to the source code and rights to copy, |
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12 # modify and redistribute granted by the license, users are provided only |
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13 # with a limited warranty and the software's author, the holder of the |
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14 # economic rights, and the successive licensors have only limited |
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15 # liability. |
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16 # |
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17 # In this respect, the user's attention is drawn to the risks associated |
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18 # with loading, using, modifying and/or developing or reproducing the |
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19 # software by the user in light of its specific status of free software, |
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20 # that may mean that it is complicated to manipulate, and that also |
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21 # therefore means that it is reserved for developers and experienced |
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22 # professionals having in-depth computer knowledge. Users are therefore |
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23 # encouraged to load and test the software's suitability as regards their |
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24 # requirements in conditions enabling the security of their systems and/or |
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25 # data to be ensured and, more generally, to use and operate it in the |
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26 # same conditions as regards security. |
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27 # |
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28 # The fact that you are presently reading this means that you have had |
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29 # knowledge of the CeCILL license and that you accept its terms. |
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30 |
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31 |
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32 import sys |
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33 import re |
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34 from commons.core.seq.Bioseq import Bioseq |
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35 from commons.core.stat.Stat import Stat |
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36 |
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37 |
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38 ## Handle a collection of a Bioseq (header-sequence) |
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39 # |
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40 class BioseqDB( object ): |
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41 |
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42 def __init__( self, name="" ): |
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43 self.idx = {} |
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44 self.idx_renamed = {} |
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45 self.db = [] |
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46 self.name = name |
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47 if name != "": |
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48 faFile = open( name ) |
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49 self.read( faFile ) |
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50 faFile.close() |
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51 self.mean_seq_lgth = None |
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52 self.stat = Stat() |
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53 |
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54 |
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55 ## Equal operator |
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56 # |
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57 def __eq__( self, o ): |
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58 selfSize = self.getSize() |
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59 if selfSize != o.getSize(): |
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60 return False |
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61 nbEqualInstances = 0 |
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62 for i in self.db: |
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63 atLeastOneIsEqual = False |
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64 for j in o.db: |
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65 if i == j: |
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66 atLeastOneIsEqual = True |
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67 continue |
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68 if atLeastOneIsEqual: |
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69 nbEqualInstances += 1 |
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70 if nbEqualInstances == selfSize: |
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71 return True |
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72 return False |
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73 |
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74 |
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75 ## Change the name of the BioseqDB |
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76 # |
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77 # @param name the BioseqDB name |
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78 # |
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79 def setName(self, name): |
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80 self.name = name |
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81 |
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82 |
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83 ## Record each sequence of the input file as a list of Bioseq instances |
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84 # |
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85 # @param faFileHandler handler of a fasta file |
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86 # |
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87 def read( self, faFileHandler ): |
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88 while True: |
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89 seq = Bioseq() |
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90 seq.read( faFileHandler ) |
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91 if seq.sequence == None: |
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92 break |
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93 self.add( seq ) |
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94 |
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95 |
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96 ## Write all Bioseq of BioseqDB in a formatted fasta file (60 character long) |
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97 # |
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98 # @param faFileHandler file handler of a fasta file |
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99 # |
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100 def write( self, faFileHandler ): |
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101 for bs in self.db: |
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102 bs.writeABioseqInAFastaFile( faFileHandler ) |
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103 |
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104 |
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105 ## Write all Bioseq of BioseqDB in a formatted fasta file (60 character long) |
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106 # |
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107 # @param outFaFileName file name of fasta file |
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108 # @param mode 'write' or 'append' |
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109 # |
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110 def save( self, outFaFileName, mode="w" ): |
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111 outFaFile = open( outFaFileName, mode ) |
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112 self.write( outFaFile ) |
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113 outFaFile.close() |
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114 |
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115 |
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116 ## Read a formatted fasta file and load it in the BioseqDB instance |
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117 # |
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118 # @param inFaFileName file name of fasta file |
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119 # |
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120 def load(self, inFaFileName): |
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121 fichier = open(inFaFileName) |
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122 self.read(fichier) |
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123 fichier.close() |
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124 |
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125 |
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126 ## Reverse each sequence of the collection |
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127 # |
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128 def reverse( self ): |
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129 for bs in self.db: |
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130 bs.reverse() |
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131 |
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132 |
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133 ## Turn each sequence into its complement |
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134 # |
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135 def complement( self ): |
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136 for bs in self.db: |
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137 bs.complement() |
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138 |
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139 |
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140 ## Reverse and complement each sequence |
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141 # |
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142 def reverseComplement( self ): |
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143 for bs in self.db: |
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144 bs.reverseComplement() |
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145 |
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146 |
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147 ## Set the collection from a list of Bioseq instances |
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148 # |
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149 def setData( self, lBioseqs ): |
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150 for i in lBioseqs: |
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151 self.add( i ) |
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152 |
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153 |
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154 ## Initialization of each attribute of the collection |
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155 # |
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156 def reset( self ): |
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157 self.db = [] |
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158 self.idx = {} |
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159 self.name = None |
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160 self.mean_seq_lgth = None |
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161 self.stat.reset() |
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162 |
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163 |
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164 ## Remove all the gap of the sequences of the collection |
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165 # |
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166 def cleanGap(self): |
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167 for iBioSeq in self.db: |
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168 iBioSeq.cleanGap() |
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169 |
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170 |
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171 ## Add a Bioseq instance and update the attributes |
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172 # |
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173 # @param bs a Bioseq instance |
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174 # |
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175 def add( self, bs ): |
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176 if self.idx.has_key( bs.header ): |
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177 sys.stderr.write( "ERROR: two sequences with same header '%s'\n" % ( bs.header ) ) |
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178 sys.exit(1) |
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179 self.db.append( bs ) |
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180 self.idx[ bs.header ] = len(self.db) - 1 |
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181 self.idx_renamed[ bs.header.replace("::","-").replace(":","-").replace(",","-").replace(" ","_") ] = len(self.db) - 1 |
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182 |
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183 |
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184 ## Give the Bioseq instance corresponding to specified index |
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185 # |
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186 # @return a Bioseq instance |
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187 # |
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188 def __getitem__(self,index): |
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189 if index < len(self.db): |
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190 return self.db[index] |
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191 |
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192 |
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193 ## Give the number of sequences in the bank |
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194 # |
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195 # @return an integer |
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196 # |
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197 def getSize( self ): |
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198 return len( self.db ) |
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199 |
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200 |
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201 ## Give the cumulative sequence length in the bank |
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202 # |
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203 # @return an integer |
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204 # |
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205 def getLength( self ): |
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206 cumLength = 0 |
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207 for iBioseq in self.db: |
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208 cumLength += iBioseq.getLength() |
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209 |
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210 return cumLength |
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211 |
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212 |
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213 ## Return the length of a given sequence via its header |
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214 # |
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215 # @return an integer |
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216 # |
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217 def getSeqLength( self, header ): |
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218 return self.fetch(header).getLength() |
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219 |
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220 |
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221 ## Return a list with the sequence headers |
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222 # |
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223 def getHeaderList( self ): |
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224 lHeaders = [] |
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225 for bs in self.db: |
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226 lHeaders.append( bs.header ) |
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227 return lHeaders |
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228 |
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229 |
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230 ## Return a list with the sequences |
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231 # |
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232 def getSequencesList( self ): |
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233 lSeqs = [] |
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234 for bs in self.db: |
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235 lSeqs.append( bs.getSequence() ) |
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236 return lSeqs |
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237 |
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238 |
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239 ## Give the Bioseq instance of the BioseqDB specified by its header |
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240 # |
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241 # @warning name of this method not appropriate getBioseqByHeader is proposed |
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242 # @param header string |
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243 # @return a Bioseq instance |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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244 # |
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245 def fetch( self, header ): |
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246 return self.db[self.idx[header]] |
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247 |
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248 |
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249 ## Give the Bioseq instance of the BioseqDB specified by its renamed header |
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250 # In renamed header "::", ":", "," character are been replaced by "-" and " " by "_" |
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251 # |
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252 # @param renamedHeader string |
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253 # @return a Bioseq instance |
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254 # |
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255 def getBioseqByRenamedHeader( self, renamedHeader ): |
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256 return self.db[self.idx_renamed[renamedHeader]] |
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257 |
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258 |
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259 ## Count the number of times the given nucleotide is present in the bank. |
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260 # |
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261 # @param nt character (nt or aa) |
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262 # @return an integer |
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263 # |
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264 def countNt( self, nt ): |
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265 total = 0 |
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266 for iBioseq in self.db: |
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267 total+= iBioseq.countNt( nt ) |
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268 return total |
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269 |
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270 |
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271 ## Count the number of times each nucleotide (A,T,G,C,N) is present in the bank. |
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272 # |
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273 # @return a dictionary with nucleotide as key and an integer as values |
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274 # |
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275 def countAllNt( self ): |
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276 dNt2Count = {} |
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277 for nt in ["A","T","G","C","N"]: |
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278 dNt2Count[ nt ] = self.countNt( nt ) |
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279 return dNt2Count |
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280 |
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281 |
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282 ## Extract a sub BioseqDB of specified size which beginning at specified start |
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283 # |
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284 # @param start integer index of first included Bioseq |
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285 # @param size integer size of expected BioseqDB |
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286 # @return a BioseqDB |
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287 # |
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288 def extractPart(self, start, size): |
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289 iShorterBioseqDB = BioseqDB() |
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290 for iBioseq in self.db[start:(start + size)]: |
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291 iShorterBioseqDB.add(iBioseq) |
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292 return iShorterBioseqDB |
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293 |
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294 |
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295 ## Extract a sub BioseqDB with the specified number of best length Bioseq |
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296 # |
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297 # @param numBioseq integer the number of Bioseq searched |
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298 # @return a BioseqDB |
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299 # |
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300 def bestLength(self, numBioseq): |
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301 length_list = [] |
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302 numseq = 0 |
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303 for each_seq in self.db: |
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304 if each_seq.sequence == None: |
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305 l=0 |
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306 else: |
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307 l = each_seq.getLength() |
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308 length_list.append(l) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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309 numseq = numseq + 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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310 |
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311 length_list.sort() |
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312 size = len(length_list) |
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313 if numBioseq < size: |
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314 len_min = length_list[size-numBioseq] |
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315 else: |
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316 len_min = length_list[0] |
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317 |
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318 numseq = 0 |
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319 nbsave = 0 |
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320 bestSeqs = BioseqDB() |
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321 bestSeqs.setName(self.name) |
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322 for each_seq in self.db: |
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323 if each_seq.sequence == None: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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324 l=0 |
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325 else : |
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326 l = each_seq.getLength() |
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327 numseq = numseq + 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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328 if l >= len_min: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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329 bestSeqs.add(each_seq) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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330 nbsave = nbsave + 1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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331 if nbsave == numBioseq : |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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332 break |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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333 return bestSeqs |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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334 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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335 |
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336 ## Extract a sub BioseqDB from a file with Bioseq header containing the specified pattern |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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337 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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338 # @param pattern regular expression of wished Bioseq header |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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339 # @param inFileName name of fasta file in which we want extract the BioseqDB |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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340 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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341 def extractPatternOfFile(self, pattern, inFileName): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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342 if pattern=="" : |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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343 return |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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344 srch=re.compile(pattern) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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345 file_db=open(inFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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346 numseq=0 |
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347 nbsave=0 |
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348 while 1: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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349 seq=Bioseq() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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350 seq.read(file_db) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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351 if seq.sequence==None: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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352 break |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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353 numseq+=1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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354 m=srch.search(seq.header) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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355 if m: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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356 self.add(seq) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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357 nbsave+=1 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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358 file_db.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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359 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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360 |
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361 ## Extract a sub BioseqDB from the instance with all Bioseq header containing the specified pattern |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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362 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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363 # @param pattern regular expression of wished Bioseq header |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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364 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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365 # @return a BioseqDB |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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366 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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367 def getByPattern(self,pattern): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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368 if pattern=="" : |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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369 return |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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370 iBioseqDB=BioseqDB() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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371 srch=re.compile(pattern) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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372 for iBioseq in self.db: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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373 if srch.search(iBioseq.header): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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374 iBioseqDB.add(iBioseq) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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375 return iBioseqDB |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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376 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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377 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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378 ## Extract a sub BioseqDB from the instance with all Bioseq header not containing the specified pattern |
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379 # |
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380 # @param pattern regular expression of not wished Bioseq header |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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381 # |
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382 # @return a BioseqDB |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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383 # |
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384 def getDiffFromPattern(self,pattern): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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385 if pattern=="" : |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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386 return |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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387 iBioseqDB=BioseqDB() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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388 srch=re.compile(pattern) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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389 for iBioseq in self.db: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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390 if not srch.search(iBioseq.header): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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391 iBioseqDB.add(iBioseq) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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392 return iBioseqDB |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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393 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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394 #TODO: to run several times to remove all concerned sequences when big data. How to fix it ? |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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395 ## Remove from the instance all Bioseq which header contains the specified pattern |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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396 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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397 # @param pattern regular expression of not wished Bioseq header |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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398 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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399 def rmByPattern(self,pattern): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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400 if pattern=="" : |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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401 return |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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402 srch=re.compile(pattern) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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403 for seq in self.db: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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404 if srch.search(seq.header): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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405 self.db.remove(seq) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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406 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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407 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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408 ## Copy a part from another BioseqDB in the BioseqDB if Bioseq have got header containing the specified pattern |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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409 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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410 # @warning this method is called extractPattern in pyRepet.seq.BioseqDB |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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411 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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412 # @param pattern regular expression of wished Bioseq header |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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413 # @param sourceBioseqDB the BioseqDB from which we want extract Bioseq |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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414 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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415 def addBioseqFromABioseqDBIfHeaderContainPattern(self, pattern, sourceBioseqDB): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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416 if pattern=="" : |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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417 return |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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418 srch=re.compile(pattern) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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419 for seq in sourceBioseqDB.db: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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420 m=srch.search(seq.header) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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421 if m: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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422 self.add(seq) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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423 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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424 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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425 ## Up-case the sequence characters in all sequences |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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426 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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427 def upCase( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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428 for bs in self.db: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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429 bs.upCase() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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430 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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431 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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432 ## Split each gapped Bioseq in a list and store all in a dictionary |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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433 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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434 # @return a dict, keys are bioseq headers, values are list of Map instances |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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435 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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436 def getDictOfLMapsWithoutGaps( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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437 dSeq2Maps = {} |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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438 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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439 for bs in self.db: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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440 dSeq2Maps[ bs.header ] = bs.getLMapWhithoutGap() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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441 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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442 return dSeq2Maps |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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443 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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444 ## Give the list of the sequence length in the bank |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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445 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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446 # @return an list |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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447 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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448 def getListOfSequencesLength( self ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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449 lLength = [] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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parents:
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450 for iBioseq in self.db: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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451 lLength.append(iBioseq.getLength()) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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452 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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453 return lLength |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
454 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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455 ## Return sequence length for a list of sequence header |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
456 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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457 def getSeqLengthByListOfName( self, lHeaderName ): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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458 lseqLength=[] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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459 for headerName in lHeaderName: |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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460 lseqLength.append(self.getSeqLength( headerName )) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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461 return lseqLength |