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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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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 import os, os.path, struct
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32 from commons.core.parsing.GffParser import GffParser
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33 from SMART.Java.Python.misc.Progress import Progress
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34
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35
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36 class Data(object):
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37 def __init__(self, hIndex, transcript, firstChildLIndex, lastChildLIndex, start, end):
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38 self.hIndex = hIndex
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39 self.transcript = transcript
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40 self.firstChildLIndex = firstChildLIndex
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41 self.lastChildLIndex = lastChildLIndex
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42 self.start = start
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43 self.end = end
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44
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45 class NCListCursor(object):
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46
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47 def __init__(self, cursor = None, ncList = None, lIndex = 0, verbosity = 0):
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48 self._verbosity = verbosity
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49 self._mainListData = []
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50 if cursor:
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51 self.copy(cursor)
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52 else:
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53 self._ncList = ncList
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54 self.setLIndex(lIndex)
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55
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56 def setLIndex(self, lIndex):
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57 self._lIndex = lIndex
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58 self._start = None
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59 self._end = None
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60 self._hIndex = None
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61 self._gffIndex = None
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62 self._parentGffIndex = None
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63 self._parentLIndex = None
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64 self._parentHIndex = None
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65 self._parentStart = None
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66 self._parentEnd = None
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67 self._transcript = None
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68 self._firstSiblingLIndex = None
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69 self._lastSiblingLIndex = None
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70 self._firstChildLIndex = None
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71 self._lastChildLIndex = None
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72 self._mainListIndex = lIndex if lIndex < self._ncList.getSizeFirstList() else None
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73
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74 def precompute(self):
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75 self._mainListIndex = 0
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76 progress = Progress(self._ncList.getSizeFirstList(), "Precomputing data", self._verbosity)
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77 for i in range(self._ncList.getSizeFirstList()):
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78 gffIndex, hIndex, parentLIndex, start, end = self._ncList.getLLineElements(i)
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79 transcript = self._ncList.getIntervalFromAdress(gffIndex)
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80 firstChildLIndex, nbChildren = self._ncList.getHLineElements(hIndex)
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81 lastChildLIndex = -1 if firstChildLIndex == -1 else firstChildLIndex + nbChildren-1
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82 self._mainListData.append(Data(hIndex, transcript, firstChildLIndex, lastChildLIndex, start, end))
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83 progress.inc()
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84 progress.done()
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85
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86 def _updateFromMainListData(self):
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87 if not self._mainListData or self._lIndex >= self._ncList.getSizeFirstList():
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88 #print "OUT"
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89 return False
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90 if self._mainListIndex >= self._ncList.getSizeFirstList():
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91 self._hIndex = -1
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92 data = self._mainListData[self._mainListIndex]
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93 self._hIndex = data.hIndex
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94 self._transcript = data.transcript
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95 self._firstChildLIndex = data.firstChildLIndex
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96 self._lastChildLIndex = data.lastChildLIndex
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97 self._start = data.start
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98 self._end = data.end
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99 return True
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100
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101 def getLIndex(self):
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102 return self._lIndex
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103
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104 def _getCurrentData(self):
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105 self._gffIndex, self._hIndex, self._parentLIndex, self._start, self._end = self._ncList.getLLineElements(self._lIndex)
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106 #print "-->", self._lIndex, "-->", self._gffIndex, self._hIndex, self._parentLIndex, self._start, self._end
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107 if self._end == -1:
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108 raise Exception("Error")
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109
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110 def _getParentData(self):
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111 if self._parentLIndex == None:
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112 self._getCurrentData()
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113 self._parentGffIndex, self._parentHIndex, greatParentLIndex, self._parentStart, self._parentEnd = self._ncList.getLLineElements(self._parentLIndex)
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114
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115 def _getTranscript(self):
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116 if self._gffIndex == None:
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117 self._getCurrentData()
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118 self._transcript = self._ncList.getIntervalFromAdress(self._gffIndex)
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119
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120 def _getSiblingData(self):
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121 if self._parentHIndex == None:
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122 self._getParentData()
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123 if self._parentHIndex == -1:
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124 self._firstSiblingLIndex = 0
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125 self._lastSiblingLIndex = self._ncList.getSizeFirstList() - 1
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126 else:
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127 self._firstSiblingLIndex, nbSiblings = self._ncList.getHLineElements(self._parentHIndex)
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128 self._lastSiblingLIndex = -1 if self._firstSiblingLIndex == -1 else self._firstSiblingLIndex + nbSiblings-1
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129
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130 def _getChildrenData(self):
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131 if self._hIndex == None:
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132 self._getCurrentData()
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133 self._firstChildLIndex, nbChildren = self._ncList.getHLineElements(self._hIndex)
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134 self._lastChildLIndex = -1 if self._firstChildLIndex == -1 else self._firstChildLIndex + nbChildren-1
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135
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136 def getGffAddress(self):
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137 if self._gffIndex == None:
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138 self._getCurrentData()
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139 return self._gffIndex
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140
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141 def getStart(self):
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142 if self._start == None:
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143 self._getCurrentData()
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144 return self._start
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145
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146 def getEnd(self):
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147 if self._end == None:
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148 self._getCurrentData()
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149 return self._end
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150
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151 def compare(self, cursor):
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152 return (self._lIndex == cursor._lIndex)
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153
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154 def getTranscript(self):
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155 if self.isOut():
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156 return None
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157 if self._transcript == None:
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158 self._getTranscript()
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159 return self._transcript
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160
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161 def isFirst(self):
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162 #print "is last: ", self._lIndex, self._ncList.getSizeFirstList(), self._lastSiblingLIndex
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163 if self._lIndex < self._ncList.getSizeFirstList() - 1:
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164 return (self._lIndex == 0)
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165 if self._firstSiblingLIndex == None:
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166 self._getSiblingData()
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167 return (self._lIndex == self._firstSiblingLIndex)
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168
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169 def isLast(self):
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170 #print "is last: ", self._lIndex, self._ncList.getSizeFirstList(), self._lastSiblingLIndex
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171 if self._lIndex < self._ncList.getSizeFirstList() - 1:
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172 return (self._lIndex == self._ncList.getSizeFirstList() - 1)
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173 if self._lastSiblingLIndex == None:
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174 self._getSiblingData()
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175 return (self._lIndex == self._lastSiblingLIndex)
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176
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177 def moveUp(self):
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178 if self._parentLIndex == None:
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179 self._getCurrentData()
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180 self._lIndex = self._parentLIndex
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181 self._updateFromMainListData()
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182 self._hIndex = self._parentHIndex
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183 self._gffIndex = self._parentGffIndex
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184 self._parentLIndex = None
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185 self._parentHIndex = None
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186 self._parentGffIndex = None
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187 self._transcript = None
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188 self._firstSiblingLIndex = None
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189 self._lastSiblingLIndex = None
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190 self._firstChildLIndex = self._firstChildLIndex
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191 self._lastChildLIndex = self._lastChildLIndex
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192 self._start = self._parentStart
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193 self._end = self._parentEnd
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194 self._parentStart = None
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195 self._parentEnd = None
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196
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197 def moveRight(self):
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198 if self.isOut():
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199 return
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200 #print "IN1", self
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201 if self._lIndex < self._ncList.getSizeFirstList() - 1 and self._mainListIndex != None:
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202 self._mainListIndex += 1
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203 self._updateFromMainListData()
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204 #print "IN2", self
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205 self._lIndex += 1
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206 self._hIndex = None
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207 self._start = None
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208 self._end = None
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209 self._transcript = None
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210 self._gffIndex = None
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211 self._firstChildLIndex = None
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212 self._lastChildLIndex = None
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213 #print "IN3", self
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214
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215 def moveNext(self):
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216 while not self.isOut() and self.isLast():
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217 if self.isTop():
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218 self._lIndex = -1
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219 return
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220 self.moveUp()
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221 #print "F1", self
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222 self.moveRight()
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223 #print "F2", self
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224
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225 def moveMiddleSibling(self):
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226 if self._lIndex < self._ncList.getSizeFirstList() - 1:
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227 self._mainListIndex = (self._ncList.getSizeFirstList() - 1) / 2
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228 self._updateFromMainListData()
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229 if self._lastSiblingLIndex == None:
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230 self._getSiblingData()
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231 self._lIndex = (self._lastSiblingLIndex + self._firstSiblingLIndex) / 2
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232 self._hIndex = None
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233 self._start = None
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234 self._end = None
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235 self._gffIndex = None
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236 self._transcript = None
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237 self._firstChildLIndex = None
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238 self._lastChildLIndex = None
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239
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240 def moveSibling(self, lIndex):
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241 if self._lIndex < self._ncList.getSizeFirstList() - 1:
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242 self._mainListIndex = lIndex
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243 self._updateFromMainListData()
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244 self._lIndex = lIndex
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245 self._hIndex = None
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246 self._start = None
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247 self._end = None
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248 self._gffIndex = None
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249 self._transcript = None
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250 self._firstChildLIndex = None
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251 self._lastChildLIndex = None
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252
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253 def moveLastSibling(self):
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254 if self._lIndex < self._ncList.getSizeFirstList() - 1:
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255 self._mainListIndex = self._ncList.getSizeFirstList() - 1
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256 self._updateFromMainListData()
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257 if self._lastSiblingLIndex == None:
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258 self._getSiblingData()
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259 self._lIndex = self._lastSiblingLIndex
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260 self._hIndex = None
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261 self._start = None
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262 self._end = None
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263 self._gffIndex = None
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264 self._transcript = None
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265 self._firstChildLIndex = None
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266 self._lastChildLIndex = None
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267
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268 def moveDown(self):
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269 if self._firstChildLIndex == None:
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270 self._getChildrenData()
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271 self._parentLIndex = self._lIndex
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272 self._parentHIndex = self._hIndex
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273 self._parentGffIndex = self._gffIndex
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274 self._lIndex = self._firstChildLIndex
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275 self._lastSiblingLIndex = self._lastChildLIndex
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276 self._hIndex = None
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277 self._gffIndex = None
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278 self._transcript = None
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279 self._firstChildLIndex = None
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280 self._lastChildLIndex = None
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281 self._parentStart = self._start
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282 self._parentEnd = self._end
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283 self._start = None
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284 self._end = None
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285
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286 def isOut(self):
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287 return (self._lIndex == -1)
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288
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289 def isTop(self):
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290 if self._parentLIndex == None:
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291 self._getCurrentData()
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292 return (self._parentLIndex == -1)
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293
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294 def hasChildren(self):
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295 if self._hIndex == None:
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296 self._getCurrentData()
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297 if self._hIndex == -1:
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298 return False
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299 if self._firstChildLIndex == None:
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300 self._getChildrenData()
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301 return (self._firstChildLIndex != -1)
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302
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303 def copy(self, cursor):
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304 self._ncList = cursor._ncList
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305 self._lIndex = cursor._lIndex
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306 self._hIndex = cursor._hIndex
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307 self._gffIndex = cursor._gffIndex
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308 self._parentLIndex = cursor._parentLIndex
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309 self._parentHIndex = cursor._parentHIndex
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310 self._parentGffIndex = cursor._parentGffIndex
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311 self._transcript = cursor._transcript
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312 self._firstSiblingLIndex = cursor._firstSiblingLIndex
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313 self._lastSiblingLIndex = cursor._lastSiblingLIndex
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314 self._firstChildLIndex = cursor._firstChildLIndex
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315 self._lastChildLIndex = cursor._lastChildLIndex
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316 self._mainListData = cursor._mainListData
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317 self._mainListIndex = cursor._mainListIndex
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318 self._verbosity = cursor._verbosity
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319 self._parentStart = cursor._parentStart
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320 self._parentEnd = cursor._parentEnd
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321 self._start = cursor._start
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322 self._end = cursor._end
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323
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324 def __str__(self):
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325 return "NC-list: %s, Lindex: %s, Hindex: %s, GFFindex: %s, start: %s, end: %s, parent Lindex: %s, parent Hindex: %s, parent GFFindex: %s, transcript: %s, last sibling: %s" % (self._ncList, self._lIndex, self._hIndex, self._gffIndex, self._start, self._end, self._parentLIndex, self._parentHIndex, self._parentGffIndex, self._transcript, self._lastSiblingLIndex)
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