annotate TEisotools-1.1.a/commons/core/coord/MergedPath.py @ 15:255c852351c5 draft

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author urgi-team
date Thu, 21 Jul 2016 07:36:44 -0400
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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 import collections
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32 from commons.core.coord.Path import Path
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33 from commons.core.LoggerFactory import LoggerFactory
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34
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35 LOG_DEPTH = "repet.commons.core.coord"
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36
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37 ## Merge Path objects with the same ID in a single object
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38 #
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39 class MergedPath(object):
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40
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41 __slots__ = ("_lPaths", "_length", "_ID", "_nbPaths", "_log")
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42
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43 ## Constructor
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44 #
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45 def __init__(self, lPaths = None, verbosity = 0):
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46 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), verbosity = verbosity)
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47 self._lPaths = []
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48 self._length = 0
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49 self._ID = None
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50 self._nbPaths = 0
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51
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52 if lPaths:
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53 for p in lPaths:
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54 self.add(p)
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55
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56 ## repr
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57 #
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58 def __repr__(self):
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59 return self.toString()
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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 equal = True
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65 if type(o) is not type(self):
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66 equal = False
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67 elif self.getID() != o.getID() or self.getLength() != o.getLength() or self._nbPaths != o._nbPaths:
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68 equal = False
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69 else:
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70 equal = collections.Counter(self.getPathsList()) == collections.Counter(self.getPathsList())
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71 return equal
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72
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73 ## Not equal operator
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74 #
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75 def __ne__(self, o):
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76 return not self.__eq__(o)
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77
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78 ## Try to add a Path instance to this MergedPath instance
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79 #
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80 # @param path a Path instance
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81 #
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82 def add(self, path):
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83 if not isinstance(path, Path):
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84 msg = "Error when adding to MergedPath : Not a Path"
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85 self._log.warning(msg)
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86 elif self._ID and self._ID != path.getIdentifier():
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87 msg = "Couldn't add Path (%i) to MergedPath (%i) : Different IDs" % (path.getIdentifier(), self._ID)
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88 self._log.warning(msg)
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89 else:
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90 self._ID = path.getIdentifier()
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91 self._lPaths.append(path)
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92 self._length += path.getAlignInstance().getLengthOnQuery()
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93 self._nbPaths = len(self._lPaths)
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94
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95 ## Get the total length of the Paths in this MergedPath instance
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96 #
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97 def getLength(self):
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98 return self._length
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99
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100 ## Get the list of Paths objects in this MergedPath instance
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101 #
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102 def getPathsList(self):
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103 return self._lPaths
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104
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105 ## Get the ID of the Path
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106 #
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107 def getID(self):
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108 return self._ID
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109
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110 ## Get the number of paths (fragments)
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111 #
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112 def getNbPaths(self):
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113 return self._nbPaths
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114
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115 ## Get the weighted identity
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116 #
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117 def getWeightedIdentity(self):
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118 res = 0
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119 if self._nbPaths > 0:
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120 sumIdentity = sum((abs(path.range_query.end - path.range_query.start) + 1) * path.identity for path in self._lPaths)
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121 sumSizes = sum(abs(path.range_query.end - path.range_query.start) + 1 for path in self._lPaths)
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122 res = sumIdentity / sumSizes
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123 res = float("{0:.2f}".format(res)) # Truncate to 2 decimals
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124 return res
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125
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126 ## Return the attributes as a formatted string
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127 #
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128 def toString(self):
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129 string = "Empty MergedPath()"
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130 if self._ID:
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131 string = "ID: %i" % self._ID
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132 string += "\tLength: %i" % self._length
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133 string += "\tNbPaths: %i" % self._nbPaths
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134 string += "\tPaths:\n"
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135 string += "\n".join([p.toString() for p in self._lPaths])
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136 return string