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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 from commons.core.parsing.SequenceListParser import SequenceListParser
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32 from SMART.Java.Python.structure.Sequence import Sequence
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33 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
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34
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35 class FastaParser(SequenceListParser):
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36 """A class that reads a list of sequences in FASTA"""
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37
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38 def __init__(self, fileName, verbosity = 0):
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39 super(FastaParser, self).__init__(fileName, verbosity)
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40 self.tags = {}
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41
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42
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43 def getTags(self):
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44 return self.tags
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45
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46
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47 def getFileFormats():
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48 return ["fasta", "mfa", "fas"]
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49 getFileFormats = staticmethod(getFileFormats)
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50
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51
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52 def getInfos(self):
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53 """
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54 Get some generic information about the sequences
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55 """
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56 self.nbSequences = 0
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57 self.size = 0
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58 self.reset()
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59 progress = UnlimitedProgress(100000, "Reading input file", self.verbosity - 9)
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60 for line in self.handle:
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61 line = line.strip()
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62 if line == "":
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63 continue
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64 if line[0] == ">":
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65 self.nbSequences += 1
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66 else:
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67 self.size += len(line)
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68 progress.inc()
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69 progress.done()
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70 self.reset()
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71
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72
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73 def parseOne(self):
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74 """
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75 Parse only one element in the file
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76 """
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77 name = None
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78 string = ""
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79
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80 if self.currentLine != None:
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81 if self.currentLine[0] != ">":
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82 raise Exception("First line is weird: %s" % (self.currentLine))
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83 name = self.currentLine[1:].split()[0]
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84 self.currentLine = None
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85
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86 for line in self.handle:
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87 line = line.strip()
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88 if line == "":
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89 pass
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90 elif line[0] == ">":
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91 if name == None:
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92 name = line[1:].split()[0]
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93 else:
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94 self.currentLine = line
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95 return Sequence(name, string)
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96 else:
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97 string += line
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98
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99 if name == None:
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100 return None
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101 return Sequence(name, string)
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102
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103
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104 def setTags(self):
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105 mark = self.handle.tell()
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106 thisTag = mark
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107
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108 line = self.handle.readline()
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109 while line != "":
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110 if line[0] == ">":
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111 line = line.strip()
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112 self.tags[line[1:].split()[0]] = thisTag
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113 thisTag = self.handle.tell()
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114 line = self.handle.readline()
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115
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116 self.handle.seek(mark)
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117
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118
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119 def getSubSequence(self, chromosome, start, end, direction, name = None):
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120 if not self.tags:
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121 self.setTags()
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122
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123 if chromosome not in self.tags:
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124 raise Exception("Cannot find " + chromosome)
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125
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126 if name == None:
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127 name = "%s:%d-%d (%d)" % (chromosome, start, end, direction)
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128 sequence = Sequence(name)
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129
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130 # switch from 0-based to 1-based coordinates
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131 start -= 1
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132 end -= 1
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133
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134 self.handle.seek(self.tags[chromosome])
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135 line = self.handle.readline().strip()
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136 if line != ">" + chromosome:
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137 raise Exception("Arrived in a wrong place (got %s)" % (line))
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138
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139 position1 = self.handle.tell()
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140 line = self.handle.readline().strip()
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141 position2 = self.handle.tell()
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142 size = len(line)
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143 address = position1 + ((start - (start % size)) / size) * (position2 - position1);
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144
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145 count = max(0, start - (start % size));
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146 self.handle.seek(address)
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147
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148 newSequence = ""
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149 for line in self.handle:
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150 line = line.strip()
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151
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152 if line[0] == ">":
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153 break
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154
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155 subStart = start - count
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156 if subStart < 0:
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157 subStart = 0
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158 subEnd = end - count
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159 subSize = subEnd - subStart + 1
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160 if subSize + subStart > len(line):
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161 subSize = len(line) - subStart
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162 if subEnd < 0:
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163 break
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164 if subStart <= len(line):
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165 newSequence += line[subStart:subStart+subSize]
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166 count += len(line)
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167
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168 if newSequence == "":
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169 raise Exception("Error, sequence %s is empty" % (name))
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170 sequence.sequence = newSequence
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171 if direction == -1:
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172 sequence.reverseComplement()
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173 return sequence
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