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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 string
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34 import re
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35 import random
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36 import cStringIO
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37 from commons.core.coord.Map import Map
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18
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38 from commons.core.checker.RepetException import RepetException
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6
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39
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40 DNA_ALPHABET_WITH_N = set( ['A','T','G','C','N'] )
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41 IUPAC = set(['A','T','G','C','U','R','Y','M','K','W','S','B','D','H','V','N'])
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42
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43
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44 ## Record a sequence with its header
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45 #
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46 class Bioseq( object ):
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47
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48 header = ""
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49 sequence = ""
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50
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51 ## constructor
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52 #
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53 # @param name the header of sequence
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54 # @param seq sequence (DNA, RNA, protein)
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55 #
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56 def __init__( self, name="", seq="" ):
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57 self.header = name
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58 self.sequence = seq
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59
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60
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61 ## Equal operator
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62 #
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63 def __eq__( self, o ):
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64 if self.header==o.header and self.sequence==o.sequence:
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65 return True
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66 return False
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67
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68
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69 ## overload __repr__
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70 #
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71 def __repr__( self ):
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72 return "%s;%s" % ( self.header, self.sequence )
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73
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74
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75 ## set attribute header
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76 #
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77 # @param header a string
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78 #
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79 def setHeader( self, header ):
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80 self.header = header
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81
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82
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83 ## get attribute header
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84 #
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85 # @return header
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86 def getHeader(self):
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87 return self.header
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88
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89
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90 ## set attribute sequence
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91 #
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92 # @param sequence a string
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93 #
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94 def setSequence( self, sequence ):
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95 self.sequence = sequence
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96
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97
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98 def getSequence(self):
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99 return self.sequence
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100
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101 ## reset
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102 #
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103 def reset( self ):
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104 self.setHeader( "" )
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105 self.setSequence( "" )
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106
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107
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108 ## Test if bioseq is empty
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109 #
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110 def isEmpty( self ):
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111 return self.header == "" and self.sequence == ""
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112
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113
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114 ## Reverse the sequence
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115 #
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116 def reverse( self ):
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117 tmp = self.sequence
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118 self.sequence = tmp[::-1]
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119
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120
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121 ## Turn the sequence into its complement
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122 # Force upper case letters
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123 # @warning: old name in pyRepet.Bioseq realComplement
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124 #
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125 def complement( self ):
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126 complement = ""
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127 self.upCase()
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128 for i in xrange(0,len(self.sequence),1):
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129 if self.sequence[i] == "A":
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130 complement += "T"
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131 elif self.sequence[i] == "T":
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132 complement += "A"
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133 elif self.sequence[i] == "C":
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134 complement += "G"
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135 elif self.sequence[i] == "G":
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136 complement += "C"
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137 elif self.sequence[i] == "M":
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138 complement += "K"
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139 elif self.sequence[i] == "R":
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140 complement += "Y"
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141 elif self.sequence[i] == "W":
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142 complement += "W"
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143 elif self.sequence[i] == "S":
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144 complement += "S"
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145 elif self.sequence[i] == "Y":
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146 complement += "R"
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147 elif self.sequence[i] == "K":
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148 complement += "M"
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149 elif self.sequence[i] == "V":
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150 complement += "B"
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151 elif self.sequence[i] == "H":
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152 complement += "D"
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153 elif self.sequence[i] == "D":
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154 complement += "H"
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155 elif self.sequence[i] == "B":
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156 complement += "V"
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157 elif self.sequence[i] == "N":
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158 complement += "N"
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159 elif self.sequence[i] == "-":
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160 complement += "-"
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161 else:
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162 print "WARNING: unknown symbol '%s', replacing it by N" % ( self.sequence[i] )
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163 complement += "N"
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164 self.sequence = complement
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165
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166
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167 ## Reverse and complement the sequence
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168 #
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169 # Force upper case letters
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170 # @warning: old name in pyRepet.Bioseq : complement
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171 #
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172 def reverseComplement( self ):
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173 self.reverse()
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174 self.complement()
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175
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176
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177 ## Remove gap in the sequence
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178 #
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179 def cleanGap(self):
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180 self.sequence = self.sequence.replace("-","")
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181
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182
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183 ## Copy current Bioseq Instance
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184 #
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185 # @return: a Bioseq instance, a copy of current sequence.
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186 #
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187 def copyBioseqInstance(self):
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188 seq = Bioseq()
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189 seq.sequence = self.sequence
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190 seq.header = self.header
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191 return seq
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192
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193
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194 ## Add phase information after the name of sequence in header
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195 #
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196 # @param phase integer representing phase (1, 2, 3, -1, -2, -3)
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197 #
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198 def setFrameInfoOnHeader(self, phase):
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199 if " " in self.header:
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200 name, desc = self.header.split(" ", 1)
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201 name = name + "_" + str(phase)
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202 self.header = name + " " + desc
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203 else:
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204 self.header = self.header + "_" + str(phase)
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205
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206
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207 ## Fill Bioseq attributes with fasta file
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208 #
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209 # @param faFileHandler file handler of a fasta file
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210 #
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211 def read( self, faFileHandler ):
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212 line = faFileHandler.readline()
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213 if line == "":
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214 self.header = None
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215 self.sequence = None
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216 return
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217 while line == "\n":
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218 line = faFileHandler.readline()
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219 if line[0] == '>':
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220 self.header = string.rstrip(line[1:])
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221 else:
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222 print "error, line is",string.rstrip(line)
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223 return
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224 line = " "
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225 seq = cStringIO.StringIO()
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226 while line:
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227 prev_pos = faFileHandler.tell()
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228 line = faFileHandler.readline()
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229 if line == "":
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230 break
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231 if line[0] == '>':
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232 faFileHandler.seek( prev_pos )
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233 break
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234 seq.write( string.rstrip(line) )
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235 self.sequence = seq.getvalue()
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236
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237
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238 ## Create a subsequence with a modified header
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239 #
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240 # @param s integer start a required subsequence
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241 # @param e integer end a required subsequence
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242 #
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243 # @return a Bioseq instance, a subsequence of current sequence
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244 #
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245 def subseq( self, s, e=0 ):
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246 if e == 0 :
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247 e=len( self.sequence )
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248 if s > e :
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249 print "error: start must be < or = to end"
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250 return
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251 if s <= 0 :
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252 print "error: start must be > 0"
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253 return
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254 sub = Bioseq()
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255 sub.header = self.header + " fragment " + str(s) + ".." + str(e)
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256 sub.sequence = self.sequence[(s-1):e]
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257 return sub
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258
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259
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260 ## Get the nucleotide or aminoacid at the given position
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261 #
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262 # @param pos integer nucleotide or aminoacid position
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263 #
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264 # @return a string
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265 #
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266 def getNtFromPosition(self, pos):
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267 result = None
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268 if not (pos < 1 or pos > self.getLength()):
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269 result = self.sequence[pos - 1]
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270 return result
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271
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272
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273 ## Print in stdout the Bioseq in fasta format with 60 characters lines
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274 #
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275 # @param l length of required sequence default is whole sequence
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276 #
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277 def view(self,l=0):
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278 print '>'+self.header
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279 i=0
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280 if(l==0):
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281 l=len(self.sequence)
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282 seq=self.sequence[0:l]
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283
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284 while i<len(seq):
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285 print seq[i:i+60]
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286 i=i+60
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287
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288
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289 ## Get length of sequence
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290 #
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291 # @param avoidN boolean don't count 'N' nucleotides
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292 #
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293 # @return length of current sequence
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294 #
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295 def getLength( self, countN = True ):
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296 if countN:
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297 return len(self.sequence)
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298 else:
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299 return len(self.sequence) - self.countNt('N')
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300
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301
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302 ## Return the proportion of a specific character
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303 #
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304 # @param nt character that we want to count
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305 #
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306 def propNt( self, nt ):
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307 return self.countNt( nt ) / float( self.getLength() )
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308
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309
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310 ## Count occurrence of specific character
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311 #
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312 # @param nt character that we want to count
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313 #
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314 # @return nb of occurrences
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315 #
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316 def countNt( self, nt ):
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317 return self.sequence.count( nt )
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318
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319
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320 ## Count occurrence of each nucleotide in current seq
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321 #
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322 # @return a dict, keys are nucleotides, values are nb of occurrences
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323 #
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324 def countAllNt( self ):
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325 dNt2Count = {}
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326 for nt in ["A","T","G","C","N"]:
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327 dNt2Count[ nt ] = self.countNt( nt )
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328 return dNt2Count
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329
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330
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331 ## Return a dict with the number of occurrences for each combination of ATGC of specified size and number of word found
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332 #
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333 # @param size integer required length word
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334 #
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335 def occ_word( self, size ):
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336 occ = {}
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337 if size == 0:
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338 return occ,0
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339 nbword = 0
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340 srch = re.compile('[^ATGC]+')
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341 wordlist = self._createWordList( size )
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342 for i in wordlist:
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343 occ[i] = 0
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344 lenseq = len(self.sequence)
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345 i = 0
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346 while i < lenseq-size+1:
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347 word = self.sequence[i:i+size].upper()
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348 m = srch.search(word)
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349 if m == None:
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350 occ[word] = occ[word]+1
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351 nbword = nbword + 1
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352 i = i + 1
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353 else:
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354 i = i + m.end(0)
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355 return occ, nbword
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356
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357
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358 ## Return a dictionary with the frequency of occurs for each combination of ATGC of specified size
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359 #
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360 # @param size integer required length word
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361 #
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362 def freq_word( self, size ):
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363 dOcc, nbWords = self.occ_word( size )
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364 freq = {}
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365 for word in dOcc.keys():
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366 freq[word] = float(dOcc[word]) / nbWords
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367 return freq
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368
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369
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370 ## Find ORF in each phase
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371 #
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372 # @return: a dict, keys are phases, values are stop codon positions.
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373 #
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374 def findORF (self):
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375 orf = {0:[],1:[],2:[]}
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376 length = len (self.sequence)
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377 for i in xrange(0,length):
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378 triplet = self.sequence[i:i+3]
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379 if ( triplet == "TAA" or triplet == "TAG" or triplet == "TGA"):
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380 phase = i % 3
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381 orf[phase].append(i)
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382 return orf
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383
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384
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385 ## Convert the sequence into upper case
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386 #
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387 def upCase( self ):
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388 self.sequence = self.sequence.upper()
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389
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390
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391 ## Convert the sequence into lower case
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392 #
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393 def lowCase( self ):
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394 self.sequence = self.sequence.lower()
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395
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396
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397 ## Extract the cluster of the fragment (output from Grouper)
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398 #
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399 # @return cluster id (string)
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400 #
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401 def getClusterID( self ):
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402 data = self.header.split()
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403 return data[0].split("Cl")[1]
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404
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405
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406 ## Extract the group of the sequence (output from Grouper)
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407 #
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408 # @return group id (string)
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409 #
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410 def getGroupID( self ):
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411 data = self.header.split()
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412 return data[0].split("Gr")[1].split("Cl")[0]
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413
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414
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415 ## Get the header of the full sequence (output from Grouper)
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416 #
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417 # @example 'Dmel_Grouper_3091_Malign_3:LARD' from '>MbS1566Gr81Cl81 Dmel_Grouper_3091_Malign_3:LARD {Fragment} 1..5203'
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418 # @return header (string)
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419 #
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420 def getHeaderFullSeq( self ):
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421 data = self.header.split()
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422 return data[1]
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423
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424
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425 ## Get the strand of the fragment (output from Grouper)
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426 #
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427 # @return: strand (+ or -)
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428 #
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429 def getFragStrand( self ):
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430 data = self.header.split()
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431 coord = data[3].split("..")
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432 if int(coord[0]) < int(coord[-1]):
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433 return "+"
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434 else:
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435 return "-"
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436
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437
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438 ## Get A, T, G, C or N from an IUPAC letter
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439 # IUPAC = ['A','T','G','C','U','R','Y','M','K','W','S','B','D','H','V','N']
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440 #
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441 # @return A, T, G, C or N
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442 #
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443 def getATGCNFromIUPAC( self, nt ):
|
|
|
444 subset = ["A","T","G","C","N"]
|
|
|
445
|
|
|
446 if nt in subset:
|
|
|
447 return nt
|
|
|
448 elif nt == "U":
|
|
|
449 return "T"
|
|
|
450 elif nt == "R":
|
|
|
451 return random.choice( "AG" )
|
|
|
452 elif nt == "Y":
|
|
|
453 return random.choice( "CT" )
|
|
|
454 elif nt == "M":
|
|
|
455 return random.choice( "CA" )
|
|
|
456 elif nt == "K":
|
|
|
457 return random.choice( "TG" )
|
|
|
458 elif nt == "W":
|
|
|
459 return random.choice( "TA" )
|
|
|
460 elif nt == "S":
|
|
|
461 return random.choice( "CG" )
|
|
|
462 elif nt == "B":
|
|
|
463 return random.choice( "CTG" )
|
|
|
464 elif nt == "D":
|
|
|
465 return random.choice( "ATG" )
|
|
|
466 elif nt == "H":
|
|
|
467 return random.choice( "ATC" )
|
|
|
468 elif nt == "V":
|
|
|
469 return random.choice( "ACG" )
|
|
|
470 else:
|
|
|
471 return "N"
|
|
18
|
472
|
|
|
473 ## Get nucleotide from an IUPAC letter and a nucleotide
|
|
|
474 # Works only for IUPAC code with two possibilities ['R','Y','M','K','W','S']
|
|
|
475 # Examples:
|
|
|
476 # Y and C returns T
|
|
|
477 # Y and T returns C
|
|
|
478 # B and C throws RepetException
|
|
|
479 #
|
|
|
480 # @return A, T, G, C
|
|
|
481 #
|
|
|
482 def getATGCNFromIUPACandATGCN(self, IUPACCode, nt):
|
|
|
483 if IUPACCode == "R":
|
|
|
484 possibleNt = set(["A", "G"])
|
|
|
485 if nt not in possibleNt:
|
|
|
486 raise RepetException("IUPAC code '%s' and nucleotide '%s' are not compatible" % (IUPACCode, nt))
|
|
|
487 return (possibleNt - set(nt)).pop()
|
|
6
|
488
|
|
18
|
489 elif IUPACCode == "Y":
|
|
|
490 possibleNt = set(["C", "T"])
|
|
|
491 if nt not in possibleNt:
|
|
|
492 raise RepetException("IUPAC code '%s' and nucleotide '%s' are not compatible" % (IUPACCode, nt))
|
|
|
493 return (possibleNt - set(nt)).pop()
|
|
6
|
494
|
|
18
|
495 elif IUPACCode == "M":
|
|
|
496 possibleNt = set(["A", "C"])
|
|
|
497 if nt not in possibleNt:
|
|
|
498 raise RepetException("IUPAC code '%s' and nucleotide '%s' are not compatible" % (IUPACCode, nt))
|
|
|
499 return (possibleNt - set(nt)).pop()
|
|
|
500
|
|
|
501 elif IUPACCode == "K":
|
|
|
502 possibleNt = set(["T", "G"])
|
|
|
503 if nt not in possibleNt:
|
|
|
504 raise RepetException("IUPAC code '%s' and nucleotide '%s' are not compatible" % (IUPACCode, nt))
|
|
|
505 return (possibleNt - set(nt)).pop()
|
|
|
506
|
|
|
507 elif IUPACCode == "W":
|
|
|
508 possibleNt = set(["A", "T"])
|
|
|
509 if nt not in possibleNt:
|
|
|
510 raise RepetException("IUPAC code '%s' and nucleotide '%s' are not compatible" % (IUPACCode, nt))
|
|
|
511 return (possibleNt - set(nt)).pop()
|
|
|
512
|
|
|
513 elif IUPACCode == "S":
|
|
|
514 possibleNt = set(["C", "G"])
|
|
|
515 if nt not in possibleNt:
|
|
|
516 raise RepetException("IUPAC code '%s' and nucleotide '%s' are not compatible" % (IUPACCode, nt))
|
|
|
517 return (possibleNt - set(nt)).pop()
|
|
|
518
|
|
|
519 else:
|
|
|
520 raise RepetException("Can't retrieve the third nucleotide from IUPAC code '%s' and nucleotide '%s'" % (IUPACCode, nt))
|
|
|
521
|
|
6
|
522 def getSeqWithOnlyATGCN( self ):
|
|
|
523 newSeq = ""
|
|
|
524 for nt in self.sequence:
|
|
|
525 newSeq += self.getATGCNFromIUPAC( nt )
|
|
|
526 return newSeq
|
|
|
527
|
|
|
528
|
|
|
529 ## Replace any symbol not in (A,T,G,C,N) by another nucleotide it represents
|
|
|
530 #
|
|
|
531 def partialIUPAC( self ):
|
|
|
532 self.sequence = self.getSeqWithOnlyATGCN()
|
|
|
533
|
|
|
534
|
|
|
535 ## Remove non Unix end-of-line symbols, if any
|
|
|
536 #
|
|
|
537 def checkEOF( self ):
|
|
|
538 symbol = "\r" # corresponds to '^M' from Windows
|
|
|
539 if symbol in self.sequence:
|
|
|
540 print "WARNING: Windows EOF removed in '%s'" % ( self.header )
|
|
|
541 sys.stdout.flush()
|
|
|
542 newSeq = self.sequence.replace( symbol, "" )
|
|
|
543 self.sequence = newSeq
|
|
|
544
|
|
|
545
|
|
|
546 ## Write Bioseq instance into a fasta file handler
|
|
|
547 #
|
|
|
548 # @param faFileHandler file handler of a fasta file
|
|
|
549 #
|
|
|
550 def write( self, faFileHandler ):
|
|
|
551 faFileHandler.write( ">%s\n" % ( self.header ) )
|
|
|
552 self.writeSeqInFasta( faFileHandler )
|
|
|
553
|
|
|
554
|
|
|
555 ## Write only the sequence of Bioseq instance into a fasta file handler
|
|
|
556 #
|
|
|
557 # @param faFileHandler file handler of a fasta file
|
|
|
558 #
|
|
|
559 def writeSeqInFasta( self, faFileHandler ):
|
|
|
560 i = 0
|
|
|
561 while i < self.getLength():
|
|
|
562 faFileHandler.write( "%s\n" % ( self.sequence[i:i+60] ) )
|
|
|
563 i += 60
|
|
|
564
|
|
|
565
|
|
|
566 ## Append Bioseq instance to a fasta file
|
|
|
567 #
|
|
|
568 # @param faFile name of a fasta file as a string
|
|
|
569 # @param mode 'write' or 'append'
|
|
|
570 #
|
|
|
571 def save( self, faFile, mode="a" ):
|
|
|
572 faFileHandler = open( faFile, mode )
|
|
|
573 self.write( faFileHandler )
|
|
|
574 faFileHandler.close()
|
|
|
575
|
|
|
576
|
|
|
577 ## Append Bioseq instance to a fasta file
|
|
|
578 #
|
|
|
579 # @param faFile name of a fasta file as a string
|
|
|
580 #
|
|
|
581 def appendBioseqInFile( self, faFile ):
|
|
|
582 self.save( faFile, "a" )
|
|
|
583
|
|
|
584
|
|
|
585 ## Write Bioseq instance into a fasta file handler
|
|
|
586 #
|
|
|
587 # @param faFileHandler file handler on a file with writing right
|
|
|
588 #
|
|
|
589 def writeABioseqInAFastaFile( self, faFileHandler ):
|
|
|
590 self.write( faFileHandler )
|
|
|
591
|
|
|
592
|
|
|
593 ## Write Bioseq instance with other header into a fasta file handler
|
|
|
594 #
|
|
|
595 # @param faFileHandler file handler on a file with writing right
|
|
|
596 # @param otherHeader a string representing a new header (without the > and the \n)
|
|
|
597 #
|
|
|
598 def writeWithOtherHeader( self, faFileHandler, otherHeader ):
|
|
|
599 self.header = otherHeader
|
|
|
600 self.write( faFileHandler )
|
|
|
601
|
|
|
602
|
|
|
603 ## Append Bioseq header and Bioseq sequence in a fasta file
|
|
|
604 #
|
|
|
605 # @param faFileHandler file handler on a file with writing right
|
|
|
606 # @param otherHeader a string representing a new header (without the > and the \n)
|
|
|
607 #
|
|
|
608 def writeABioseqInAFastaFileWithOtherHeader( self, faFileHandler, otherHeader ):
|
|
|
609 self.writeWithOtherHeader( faFileHandler, otherHeader )
|
|
|
610
|
|
|
611
|
|
|
612 ## get the list of Maps corresponding to seq without gap
|
|
|
613 #
|
|
|
614 # @warning This method was called getMap() in pyRepet.Bioseq
|
|
|
615 # @return a list of Map object
|
|
|
616 #
|
|
|
617 def getLMapWhithoutGap( self ):
|
|
|
618 lMaps = []
|
|
|
619 countSite = 1
|
|
|
620 countSubseq = 1
|
|
|
621 inGap = False
|
|
|
622 startMap = -1
|
|
|
623 endMap = -1
|
|
|
624
|
|
|
625 # initialize with the first site
|
|
|
626 if self.sequence[0] == "-":
|
|
|
627 inGap = True
|
|
|
628 else:
|
|
|
629 startMap = countSite
|
|
|
630
|
|
|
631 # for each remaining site
|
|
|
632 for site in self.sequence[1:]:
|
|
|
633 countSite += 1
|
|
|
634
|
|
|
635 # if it is a gap
|
|
|
636 if site == "-":
|
|
|
637
|
|
|
638 # if this is the beginning of a gap, record the previous subsequence
|
|
|
639 if inGap == False:
|
|
|
640 inGap = True
|
|
|
641 endMap = countSite - 1
|
|
|
642 lMaps.append( Map( "%s_subSeq%i" % (self.header,countSubseq), self.header, startMap, endMap ) )
|
|
|
643 countSubseq += 1
|
|
|
644
|
|
|
645 # if it is NOT a gap
|
|
|
646 if site != "-":
|
|
|
647
|
|
|
648 # if it is the end of a gap, begin the next subsequence
|
|
|
649 if inGap == True:
|
|
|
650 inGap = False
|
|
|
651 startMap = countSite
|
|
|
652
|
|
|
653 # if it is the last site
|
|
|
654 if countSite == self.getLength():
|
|
|
655 endMap = countSite
|
|
|
656 lMaps.append( Map( "%s_subSeq%i" % (self.header,countSubseq), self.header, startMap, endMap ) )
|
|
|
657
|
|
|
658 return lMaps
|
|
|
659
|
|
|
660
|
|
|
661 ## get the percentage of GC
|
|
|
662 #
|
|
|
663 # @return a percentage
|
|
|
664 #
|
|
|
665 def getGCpercentage( self ):
|
|
|
666 tmpSeq = self.getSeqWithOnlyATGCN()
|
|
|
667 nbGC = tmpSeq.count( "G" ) + tmpSeq.count( "C" )
|
|
|
668 return 100 * nbGC / float( self.getLength() )
|
|
|
669
|
|
|
670 ## get the percentage of GC of a sequence without counting N in sequence length
|
|
|
671 #
|
|
|
672 # @return a percentage
|
|
|
673 #
|
|
|
674 def getGCpercentageInSequenceWithoutCountNInLength(self):
|
|
|
675 tmpSeq = self.getSeqWithOnlyATGCN()
|
|
|
676 nbGC = tmpSeq.count( "G" ) + tmpSeq.count( "C" )
|
|
|
677 return 100 * nbGC / float( self.getLength() - self.countNt("N") )
|
|
|
678
|
|
|
679 ## get the 5 prime subsequence of a given length at the given position
|
|
|
680 #
|
|
|
681 # @param position integer
|
|
|
682 # @param flankLength integer subsequence length
|
|
|
683 # @return a sequence string
|
|
|
684 #
|
|
|
685 def get5PrimeFlank(self, position, flankLength):
|
|
|
686 if(position == 1):
|
|
|
687 return ""
|
|
|
688 else:
|
|
|
689 startOfFlank = 1
|
|
|
690 endOfFlank = position -1
|
|
|
691
|
|
|
692 if((position - flankLength) > 0):
|
|
|
693 startOfFlank = position - flankLength
|
|
|
694 else:
|
|
|
695 startOfFlank = 1
|
|
|
696
|
|
|
697 return self.subseq(startOfFlank, endOfFlank).sequence
|
|
|
698
|
|
|
699
|
|
|
700 ## get the 3 prime subsequence of a given length at the given position
|
|
|
701 # In the case of indels, the polymorphism length can be specified
|
|
|
702 #
|
|
|
703 # @param position integer
|
|
|
704 # @param flankLength integer subsequence length
|
|
|
705 # @param polymLength integer polymorphism length
|
|
|
706 # @return a sequence string
|
|
|
707 #
|
|
|
708 def get3PrimeFlank(self, position, flankLength, polymLength = 1):
|
|
|
709 if((position + polymLength) > len( self.sequence )):
|
|
|
710 return ""
|
|
|
711 else:
|
|
|
712 startOfFlank = position + polymLength
|
|
|
713
|
|
|
714 if((position+polymLength+flankLength) > len( self.sequence )):
|
|
|
715 endOfFlank = len( self.sequence )
|
|
|
716 else:
|
|
|
717 endOfFlank = position+polymLength+flankLength-1
|
|
|
718
|
|
|
719 return self.subseq(startOfFlank, endOfFlank).sequence
|
|
|
720
|
|
|
721
|
|
|
722 def _createWordList(self,size,l=['A','T','G','C']):
|
|
|
723 if size == 1 :
|
|
|
724 return l
|
|
|
725 else:
|
|
|
726 l2 = []
|
|
|
727 for i in l:
|
|
|
728 for j in ['A','T','G','C']:
|
|
|
729 l2.append( i + j )
|
|
|
730 return self._createWordList(size-1,l2)
|
|
|
731
|
|
|
732
|
|
|
733 def removeSymbol( self, symbol ):
|
|
|
734 tmp = self.sequence.replace( symbol, "" )
|
|
|
735 self.sequence = tmp
|
