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1 #
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2 # Copyright INRA-URGI 2009-2010
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3 #
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4 # This software is governed by the CeCILL license under French law and
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5 # abiding by the rules of distribution of free software. You can use,
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6 # modify and/ or redistribute the software under the terms of the CeCILL
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
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8 # "http://www.cecill.info".
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9 #
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10 # As a counterpart to the access to the source code and rights to copy,
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11 # modify and redistribute granted by the license, users are provided only
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12 # with a limited warranty and the software's author, the holder of the
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13 # economic rights, and the successive licensors have only limited
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14 # liability.
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15 #
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16 # In this respect, the user's attention is drawn to the risks associated
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17 # with loading, using, modifying and/or developing or reproducing the
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18 # software by the user in light of its specific status of free software,
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19 # that may mean that it is complicated to manipulate, and that also
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20 # therefore means that it is reserved for developers and experienced
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21 # professionals having in-depth computer knowledge. Users are therefore
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22 # encouraged to load and test the software's suitability as regards their
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23 # requirements in conditions enabling the security of their systems and/or
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24 # data to be ensured and, more generally, to use and operate it in the
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25 # same conditions as regards security.
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26 #
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27 # The fact that you are presently reading this means that you have had
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28 # knowledge of the CeCILL license and that you accept its terms.
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29 #
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30 import sys
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31 import re
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32 from commons.core.seq.Bioseq import Bioseq
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33
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34 reverseComplementString = {
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35 "A": "T",
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36 "C": "G",
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37 "G": "C",
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38 "T": "A",
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39 "U": "A",
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40 "M": "K",
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41 "R": "Y",
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42 "W": "W",
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43 "S": "S",
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44 "Y": "R",
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45 "K": "M",
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46 "V": "B",
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47 "H": "D",
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48 "D": "H",
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49 "B": "V",
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50 "N": "N",
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51 "a": "t",
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52 "c": "g",
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53 "g": "c",
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54 "t": "a",
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55 "u": "a",
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56 "m": "k",
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57 "r": "y",
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58 "w": "w",
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59 "s": "s",
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60 "y": "r",
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61 "k": "m",
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62 "v": "b",
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63 "h": "d",
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64 "d": "h",
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65 "b": "v",
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66 "n": "n"
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67 }
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68
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69 class Sequence(Bioseq):
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70 """A class that codes for a sequence"""
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71
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72 def __init__(self, name = "", sequence = ""):
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73 super(Sequence, self).__init__(name, sequence)
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74 self.name = self.header
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75 self.quality = None
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76 self.chunkedSequence = None
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77 self.chunkedQuality = None
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78 self.integerQuality = False
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79
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80 def setName(self, name=""):
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81 super(Sequence, self).setHeader(name)
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82
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83 def getName(self):
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84 return self.getHeader()
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85
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86 def setSequence(self, seq=""):
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87 super(Sequence, self).setSequence(seq)
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88
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89 def setQuality(self, quality):
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90 if quality == None:
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91 self.quality = None
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92 return
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93 if " " in quality:
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94 self.quality = quality.split()
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95 self.integerQuality = True
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96 else:
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97 self.quality = list(quality)
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98
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99 def getQuality(self):
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100 if self.quality == None:
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101 return None
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102 if self.integerQuality:
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103 return " ".join(self.quality)
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104 return "".join(self.quality)
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105
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106 def getSize(self):
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107 return len(self.getSequence())
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108
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109
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110 def copy(self, sequence):
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111 self.setName(sequence.getName())
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112 self.setSequence(sequence.getSequence())
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113 self.setQuality(sequence.getQuality())
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114 self.chunkedSequence = None
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115 self.chunkedQuality = None
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116
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117
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118 def chunkSequence(self):
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119 self.chunkedSequence = []
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120 for i in range (0, self.getSize() / 60 + 1):
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121 self.chunkedSequence.append(self.getSequence()[i * 60 : min(self.getSize(), (i+1) * 60)])
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122 if self.quality != None:
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123 self.chunkedQuality = []
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124 for i in range (0, self.getSize() / 60 + 1):
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125 self.chunkedQuality.append(self.quality[i * 60 : min(self.getSize(), (i+1) * 60)])
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126
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127 def concatenate(self, seq):
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128 sequence = self.getSequence()
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129 sequence += seq.getSequence()
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130 self.setSequence(sequence)
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131 if self.quality != None:
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132 sep = " " if self.integerQuality else ""
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133 self.setQuality(self.getQuality() + sep + seq.getQuality())
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134 self.chunkedSequence = None
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135 self.chunkedQuality = None
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136
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137
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138 def printFasta(self):
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139 if self.chunkedSequence == None:
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140 self.chunkSequence()
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141 return ">%s\n%s\n" % (self.getHeader(), "\n".join(self.chunkedSequence))
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142
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143
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144 def printFastq(self):
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145 if self.chunkedSequence == None:
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146 self.chunkSequence()
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147 return "@%s\n%s\n+%s\n%s\n" % (self.getHeader(), self.getSequence(), self.getHeader(), self.getQuality())
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148
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149
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150 def reverseComplement(self):
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151 seq = ""
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152 self.chunkedSequence = None
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153 self.chunkedQuality = None
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154 for i in range(0, self.getSize()):
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155 char = self.getSequence()[i:i+1]
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156 if char not in reverseComplementString:
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157 sys.exit("Cannot understand character %s from string %s" % (char, self.getSequence()))
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158 seq = "%s%s" % (reverseComplementString[char], seq)
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159 self.setSequence(seq)
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160 if self.quality != None:
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161 self.quality = self.quality[::-1]
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162
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163
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164 def containsAmbiguousNucleotides(self):
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165 m = re.search("[^ACGTUacgtu]", self.getSequence())
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166 if m != None:
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167 return True
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168 return False
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169
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170
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171 def shrinkToFirstNucleotides(self, nbNucleotides):
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172 self.chunkedSequence = None
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173 self.chunkedQuality = None
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174 self.setSequence(self.getSequence()[0:nbNucleotides])
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175 if self.quality != None:
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176 self.quality = self.quality[0:nbNucleotides]
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177
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178
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179 def shrinkToLastNucleotides(self, nbNucleotides):
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180 self.chunkedSequence = None
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181 self.chunkedQuality = None
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182 self.setSequence(self.getSequence()[-nbNucleotides:])
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183 if self.quality != None:
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184 self.quality = self.quality[-nbNucleotides:]
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