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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 from commons.core.coord.Range import Range
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33
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34
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35 ## Record a named region on a given sequence
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36 #
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37 class Map( Range ):
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38
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39 ## Constructor
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40 #
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41 # @param name the name of the region
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42 # @param seqname the name of the sequence
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43 # @param start the start coordinate
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44 # @param end the end coordinate
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45 #
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46 def __init__(self, name="", seqname="", start=-1, end=-1):
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47 self.name = name
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48 Range.__init__( self, seqname, start, end )
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49
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50 ## Equal operator
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51 #
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52 # @param o a Map instance
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53 #
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54 def __eq__(self, o):
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55 if self.name == o.name:
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56 return Range.__eq__(self, o)
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57 return False
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58
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59 ## Return name
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60 #
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61 def getName( self ):
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62 return self.name
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63
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64 ## Set attributes from tuple
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65 #
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66 # @param tuple: a tuple with (name,seqname,start,end)
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67 #
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68 def setFromTuple(self, tuple):
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69 self.name = tuple[0]
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70 Range.setFromTuple(self, tuple[1:])
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71
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72 ## Set attributes from string
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73 #
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74 # @param string a string formatted like name<sep>seqname<sep>start<sep>end
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75 # @param sep field separator
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76 #
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77 def setFromString(self, string, sep="\t"):
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78 if string[-1] == "\n":
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79 string = string[:-1]
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80 self.setFromTuple( string.split(sep) )
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81
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82 ## Reset
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83 #
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84 def reset(self):
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85 self.setFromTuple( [ "", "", -1, -1 ] )
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86
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87 ## Read attributes from a Map file
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88 #
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89 # @param fileHandler: file handler of the file being read
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90 # @return: 1 on success, 0 at the end of the file
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91 #
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92 def read(self, fileHandler):
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93 self.reset()
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94 line = fileHandler.readline()
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95 if line == "":
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96 return 0
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97 tokens = line.split("\t")
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98 if len(tokens) < len(self.__dict__.keys()):
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99 return 0
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100 self.setFromTuple(tokens)
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101 return 1
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102
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103 ## Return the attributes as a formatted string
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104 #
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105 def toString(self):
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106 string = "%s" % (self.name)
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107 string += "\t%s" % (Range.toString(self))
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108 return string
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109
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110 ## Write attributes into a Map file
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111 #
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112 # @param fileHandler: file handler of the file being filled
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113 #
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114 def write(self, fileHandler):
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115 fileHandler.write("%s\n" % (self.toString()))
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116
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117 ## Save attributes into a Map file
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118 #
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119 # @param file: name of the file being filled
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120 #
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121 def save(self, file):
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122 fileHandler = open( file, "a" )
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123 self.write( fileHandler )
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124 fileHandler.close()
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125
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126 ## Return a Range instance with the attributes
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127 #
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128 def getRange(self):
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129 return Range( self.seqname, self.start, self.end)
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130
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131 ## Remove in the instance the region overlapping with another Map instance
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132 #
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133 # @param o a Map instance
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134 #
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135 def diff(self, o):
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136 iRange = Range.diff(self, o.getRange())
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137 new = Map()
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138 if not iRange.isEmpty():
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139 new.name = self.name
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140 new.seqname = self.seqname
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141 new.start = iRange.start
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142 new.end = iRange.end
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143 return new
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144
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145 ## Write attributes in a Path file, the name being the subject and the rest the Range query
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146 #
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147 # @param fileHandler: file handler of a Path file
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148 #
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149 def writeAsQueryOfPath(self, fileHandler):
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150 string = "0"
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151 string += "\t%s" % ( self.seqname )
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152 string += "\t%i" % ( self.getMin() )
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153 string += "\t%i" % ( self.getMax() )
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154 string += "\t%s" % ( self.name )
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155 string += "\t0"
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156 string += "\t0"
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157 string += "\t0.0"
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158 string += "\t0"
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159 string += "\t0"
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160 fileHandler.write( "%s\n" % ( string ) )
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161
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