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6
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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
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31 from SMART.Java.Python.structure.Bins import *
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32 from commons.core.coord.Range import Range
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33
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34 class Interval(Range):
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35 """
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36 Store a genomic interval
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37 @ivar name: name of the interval [optional]
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38 @type name: string
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39 @ivar id: id of the interval [optional]
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40 @type id: int
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41 @ivar bin: bin in which the interval should be if stored in a database [computed]
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42 @type bin: int
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43 @ival tags: information about the transcript [optional]
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44 @type tags: dict
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45 @ivar verbosity: verbosity
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46 @type verbosity: int [default: 0]
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47 """
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48
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49 def __init__(self, interval = None, verbosity = 0):
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50 """
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51 Constructor
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52 @param interval: interval to be copied
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53 @type interval: class L{Interval<Interval>}
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54 @param verbosity: verbosity
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55 @type verbosity: int
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56 """
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57 Range.__init__(self)
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58 self.name = None
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59 self.id = None
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60 self.bin = None
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61 self.verbosity = verbosity
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62 self.tags = {}
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63 if interval != None:
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64 self.copy(interval)
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65
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66 #!!!! Warning: two methods getStart() and getEnd() give the information maximum and minimum in interval.!!!!#
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67 #In case strand = "+", start < end; strand = "-", start > end
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68 def getStart(self):
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69 if self.start == -1:
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70 return -1
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71 if self.end == -1:
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72 return self.start
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73 return self.getMin()
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74
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75
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76 def getEnd(self):
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77 if self.end == -1:
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78 return -1
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79 if self.start == -1:
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80 return self.end
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81 return self.getMax()
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82
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83
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84 def getChromosome(self):
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85 return self.getSeqname()
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86
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87
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88 def getDirection(self):
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89 return 1 if self.getStrand() == "+" else -1
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90
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91
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92 def getName(self):
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93 return self.name
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94
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95
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96 def isSet(self):
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97 """
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98 Check if the interval is set
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99 """
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100 return self.getStart() == None and self.getEnd() == None
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101
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102
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103 def copy(self, interval):
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104 """
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105 Copy method
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106 @param interval: interval to be copied
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107 @type interval: class L{Interval<Interval>}
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108 """
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109 self.setStart(interval.getStart())
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110 self.setEnd(interval.getEnd())
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111 self.setChromosome(interval.getChromosome())
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112 self.setDirection(interval.getDirection())
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113 self.name = interval.name
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114 self.id = interval.id
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115 self.bin = interval.bin
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116 self.tags = {}
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117 for tag in interval.tags:
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118 self.tags[tag] = interval.tags[tag]
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119 self.verbosity = interval.verbosity
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120
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121
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122 def setName(self, name):
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123 """
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124 Set the name
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125 @param name: name of the interval
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126 @type name: string
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127 """
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128 if len(name) > 100:
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129 name = name[:100]
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130 self.name = name
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131
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132
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133 def setChromosome(self, chromosome=""):
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134 """
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135 Set the chromosome
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136 @param chromosome: chromosome on which the interval is
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137 @type chromosome: string
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138 """
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139 if not chromosome:
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140 self.seqname = None
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141 else:
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142 self.seqname = chromosome.replace(".", "_").replace("|", "_")
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143
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144
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145 def setStart(self, start):
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146 """
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147 Set the start point
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148 Possibly reset bin
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149 @param start: start point of the interval
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150 @type start: int
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151 """
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152 self.bin = None
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153 direction = self.getDirection()
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154 if self.start == -1:
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155 self.start = start
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156 elif self.end == -1:
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157 self.end = start
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158 else:
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159 if direction == 1:
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160 self.start = start
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161 else:
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162 self.end = start
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163 if direction == 1:
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164 self.start, self.end = min(self.start, self.end), max(self.start, self.end)
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165 else:
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166 self.start, self.end = max(self.start, self.end), min(self.start, self.end)
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167
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168
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169 def setEnd(self, end):
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170 """
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171 Set the end point
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172 Possibly reset bin
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173 @param end: end point of the interval of the interval
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174 @type end: int
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175 """
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176 self.bin = None
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177 direction = self.getDirection()
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178 if self.end == -1:
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179 self.end = end
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180 elif self.start == -1:
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181 self.start = end
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182 else:
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183 if direction == 1:
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184 self.end = end
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185 else:
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186 self.start = end
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187 if direction == 1:
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188 self.start, self.end = min(self.start, self.end), max(self.start, self.end)
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189 else:
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190 self.start, self.end = max(self.start, self.end), min(self.start, self.end)
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191
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192
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193 def setSize(self, size):
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194 """
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195 Possibly modify the end point
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196 @param size: size of the transcript
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197 @type size: int
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198 """
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199 if self.end == None and self.start != None:
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200 self.setEnd(self.start + self.getSize() - 1)
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201 elif self.start == None and self.end != None:
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202 self.setStart(self.end - self.getSize() + 1)
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203
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204
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205 def getSize(self):
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206 """
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207 Get the size
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208 """
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209 return self.getEnd() - self.getStart() + 1
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210
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211
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212 def _setDirection(self, direction):
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213 """
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214 Set the direction of the interval (connection to Range)
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215 @param direction: direction of the transcript (+ / -)
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216 @type direction: int (1 or -1)
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217 """
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218 if direction * self.getDirection() < 0:
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219 self.reverse()
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220
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221
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222 def setDirection(self, direction):
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223 """
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224 Set the direction of the interval
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225 Possibly parse different formats
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226 @param direction: direction of the transcript (+ / -)
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227 @type direction: int or string
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228 """
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229 if type(direction).__name__ == 'int':
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230 self._setDirection(direction / abs(direction))
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231 elif type(direction).__name__ == 'str':
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232 if direction == "+":
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233 self._setDirection(1)
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234 elif direction == "-":
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235 self._setDirection(-1)
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236 elif direction == "1" or direction == "-1":
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237 self._setDirection(int(direction))
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238 elif direction.lower() == "plus":
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239 self._setDirection(1)
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240 elif direction.lower() == "minus":
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241 self._setDirection(-1)
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242 else:
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243 raise Exception("Cannot understand direction %s" % (direction))
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244 else:
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245 raise Exception("Cannot understand direction %s" % (direction))
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246
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247
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248 def extendStart(self, size):
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249 """
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250 Extend the interval by the 5' end
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251 @param size: the size to be exended
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252 @type size: int
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253 """
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254 if self.getDirection() == 1:
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255 self.setStart(max(0, self.getStart() - size))
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256 else:
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257 self.setEnd(self.getEnd() + size)
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258 self.bin = None
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259
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260
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261 def extendEnd(self, size):
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262 """
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263 Extend the interval by the 3' end
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264 @param size: the size to be exended
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265 @type size: int
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266 """
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267 if self.getDirection() == 1:
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268 self.setEnd(self.getEnd() + size)
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269 else:
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270 self.setStart(max(0, self.getStart() - size))
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271 self.bin = None
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272
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273
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274 def restrictStart(self, size = 1):
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275 """
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276 Restrict the interval by some nucleotides, start from its start position
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277 Remove the exons
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278 @param size: the size to be restricted to
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279 @type size: int
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280 """
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281 if self.getDirection() == 1:
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282 self.setEnd(min(self.getEnd(), self.getStart() + size - 1))
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283 else:
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284 self.setStart(max(self.getStart(), self.getEnd() - size + 1))
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285 self.bin = None
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286
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287
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288 def restrictEnd(self, size = 1):
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289 """
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290 Restrict the interval by some nucleotides, end from its end position
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291 Remove the exons
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292 @param size: the size to be restricted to
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293 @type size: int
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294 """
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295 if self.getDirection() == 1:
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296 self.setStart(max(self.getStart(), self.getEnd() - size + 1))
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297 else:
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298 self.setEnd(min(self.getEnd(), self.getStart() + size - 1))
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299 self.bin = None
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300
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301
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302
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303 def setTagValue(self, name, value):
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304 """
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305 Set a tag
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306 @param name: name of the tag
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307 @type name: string
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308 @param value: value of the tag
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309 @type value: int or string
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310 """
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311 self.tags[name] = value
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312
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313
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314 def getTagNames(self):
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315 """
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316 Get all the names of the tags
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317 """
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318 return self.tags.keys()
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319
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320
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321 def getTagValue(self, tag):
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322 """
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323 Get the value of a tag
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324 @param tag: name of a tag
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325 @type tag: string
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326 """
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327 if tag not in self.tags:
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328 return None
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329 return self.tags[tag]
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330
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331
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332 def getTagValues(self, tagSep = "; ", fieldSep = " ", surrounder = ""):
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333 """
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334 Get the formatted tag values
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335 @param tagSep: separator between tags
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336 @type tagSep: string
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337 @param fieldSep: separator between tag name and tag value
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338 @type fieldSep: string
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339 @param surrounder: string which optionally surround values
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340 @type surrounder: string
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341 """
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342 tags = []
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343 for name in self.tags:
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344 value = self.tags[name]
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345 if value == None:
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346 continue
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347 if isinstance(value, basestring):
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348 tags.append("%s%s%s%s%s" % (name, fieldSep, surrounder, self.tags[name], surrounder))
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349 elif type(value) is int:
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350 tags.append("%s%s%s%i%s" % (name, fieldSep, surrounder, self.tags[name], surrounder))
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351 elif type(value) is float:
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352 tags.append("%s%s%s%f%s" % (name, fieldSep, surrounder, self.tags[name], surrounder))
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353 else:
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354 raise Exception("Do not know how to print '" + value + "'.")
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355 if self.getName() != None:
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356 tags.append("%s%s%s%s%s" % ("Name", fieldSep, surrounder, self.getName(), surrounder))
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357 return tagSep.join(tags)
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358
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359
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360 def setTagValues(self, tags, tagSep = "; ", fieldSep = " "):
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361 """
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362 Set the tag values using given string
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363 @param tags: the tags, concatenated
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364 @type tags: string
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365 @param tagSep: separator between tags
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366 @type tagSep: string
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367 @param fieldSep: separator between tag name and tag value
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368 @type fieldSep: string
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369 """
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370 if tags == "":
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371 self.tags = {}
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372 return
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373 for splittedTag in tags.split(tagSep):
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374 if fieldSep not in splittedTag:
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375 raise Exception("Weird field '%s' in tags '%s'" % (splittedTag, tags))
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376 tag, value = splittedTag.split(fieldSep, 1)
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377 if tag == "Name":
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378 self.setName(value)
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379 continue
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380 try:
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381 intValue = int(value)
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382 self.tags[tag] = intValue
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383 except ValueError:
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384 try:
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385 floatValue = float(value)
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386 self.tags[tag] = floatValue
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387 except ValueError:
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388 self.tags[tag] = value
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389
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390
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391 def deleteTag(self, tag):
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392 """
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393 Remove a tag
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394 @param tag: the tag to be removed
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395 @type tag: string
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396 """
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397 if tag in self.tags:
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398 del self.tags[tag]
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399
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400
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401 def setNbOccurrences(self, nbOccurrences):
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402 """
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403 Set the number of occurrences of the interval
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404 @param nbOccurrences: number of occurrences of the interval
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405 @type nbOccurrences: int
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406 """
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407 self.setTagValue("nbOccurrences", nbOccurrences)
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408
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409
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410 def setOccurrence(self, occurrence):
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411 """
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412 Set the occurrence of this interval
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413 @param occurrence: an occurrence for this transcript
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414 @type occurrence: int
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415 """
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416 self.setTagValue("occurrence", occurrence)
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417
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418 def __eq__(self, interval):
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419 """
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420 Whether two intervals are equal (start and end at same position)
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421 @param interval: object to be compared to
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422 @type interval: class L{Interval<Interval>}
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423 """
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424 if not interval:
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425 return False
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426 return self.getChromosome() == interval.getChromosome() and self.getStart() == interval.getStart() and self.getEnd() == interval.getEnd() and self.getDirection() == interval.getDirection()
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427
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428
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429 def overlapWith(self, interval, nbNucleotides = 1):
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430 """
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431 Whether two intervals overlap
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432 @param interval: object to be compared to
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433 @type interval: class L{Interval<Interval>}
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434 @param nbNucleotides: minimum number of nucleotides to declare and overlap
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435 @type nbNucleotides: int
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436 """
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437 if self.getChromosome() != interval.getChromosome():
|
|
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438 return False
|
|
|
439 return (min(self.getEnd(), interval.getEnd()) - max(self.getStart(), interval.getStart()) + 1 >= nbNucleotides)
|
|
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440
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|
|
441 def isIncludeIn(self, interval):
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442 return interval.include(self)
|
|
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443
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444
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|
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445 def include(self, interval):
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446 """
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|
|
447 Whether this interval includes the other one
|
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|
448 @param interval: object to be compared to
|
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|
449 @type interval: class L{Interval<Interval>}
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|
|
450 """
|
|
|
451 if self.getChromosome() != interval.getChromosome():
|
|
|
452 return False
|
|
|
453 return ((self.getStart() <= interval.getStart()) and (self.getEnd() >= interval.getEnd()))
|
|
|
454
|
|
|
455
|
|
|
456 def getDifference(self, interval, sameStrand = False):
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457 """
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|
|
458 Get the difference between this cluster and another one
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|
459 @param interval: object to be compared to
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|
460 @type interval: class L{Interval<Interval>}
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|
|
461 @param sameStrand: do the comparison iff the intervals are on the same strand
|
|
|
462 @type sameStrand: boolean
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|
|
463 @return: a (possibly empty) list of intervals
|
|
|
464 """
|
|
|
465 newInterval = Interval()
|
|
|
466 newInterval.copy(self)
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|
|
467 if self.getChromosome() != interval.getChromosome():
|
|
|
468 return [newInterval]
|
|
|
469 if not self.overlapWith(interval):
|
|
|
470 return [newInterval]
|
|
|
471 if sameStrand and self.getDirection() != interval.getDirection():
|
|
|
472 return [newInterval]
|
|
|
473 intervals = []
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|
|
474 if self.getStart() < interval.getStart():
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|
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475 newInterval = Interval()
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|
|
476 newInterval.copy(self)
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|
|
477 newInterval.setEnd(min(self.getEnd(), interval.getStart() - 1))
|
|
|
478 intervals.append(newInterval)
|
|
|
479 if self.getEnd() > interval.getEnd():
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|
|
480 newInterval = Interval()
|
|
|
481 newInterval.copy(self)
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|
|
482 newInterval.setStart(max(self.getStart(), interval.getEnd() + 1))
|
|
|
483 intervals.append(newInterval)
|
|
|
484 return intervals
|
|
|
485
|
|
|
486
|
|
|
487 def getIntersection(self, interval):
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|
488 """
|
|
|
489 Get the intersection between this interval and another one
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|
|
490 @param interval: object to be compared to
|
|
|
491 @type interval: class L{Interval<Interval>}
|
|
|
492 @return: an other interval
|
|
|
493 """
|
|
|
494 if not self.overlapWith(interval):
|
|
|
495 return None
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|
|
496 newInterval = Interval()
|
|
|
497 newInterval.setChromosome(self.getChromosome())
|
|
|
498 newInterval.setDirection(self.getDirection())
|
|
|
499 newInterval.setName("%s_intersect_%s" % (self.getName(), interval.getName()))
|
|
|
500 newInterval.setStart(max(self.getStart(), interval.getStart()))
|
|
|
501 newInterval.setEnd(min(self.getEnd(), interval.getEnd()))
|
|
|
502 return newInterval
|
|
|
503
|
|
|
504
|
|
|
505 def getDistance(self, interval):
|
|
|
506 """
|
|
|
507 Get the distance between two intervals (a non-negative value)
|
|
|
508 @param interval: another interval
|
|
|
509 @type interval: class L{Interval<Interval>}
|
|
|
510 """
|
|
|
511 if self.overlapWith(interval):
|
|
|
512 return 0
|
|
|
513 if self.getChromosome() != interval.getChromosome():
|
|
|
514 raise Exception("Cannot get the distance between %s and %s" % (str(self), str(interval)))
|
|
|
515 return min(abs(self.getStart() - interval.getEnd()), abs(self.getEnd() - interval.getStart()))
|
|
|
516
|
|
|
517
|
|
|
518 def getRelativeDistance(self, interval):
|
|
|
519 """
|
|
|
520 Get the distance between two intervals (negative if first interval is before)
|
|
|
521 @param interval: another interval
|
|
|
522 @type interval: class L{Interval<Interval>}
|
|
|
523 """
|
|
|
524 if self.overlapWith(interval):
|
|
|
525 return 0
|
|
|
526 if self.getChromosome() != interval.getChromosome():
|
|
|
527 raise Exception("Cannot get the distance between %s and %s" % (str(self), str(interval)))
|
|
|
528 if self.getEnd() < interval.getStart():
|
|
|
529 distance = interval.getStart() - self.getEnd()
|
|
|
530 else:
|
|
|
531 distance = interval.getEnd() - self.getStart()
|
|
|
532 distance *= self.getDirection()
|
|
|
533 return distance
|
|
|
534
|
|
|
535
|
|
|
536 def merge(self, interval, normalization = False):
|
|
|
537 """
|
|
|
538 Merge two intervals
|
|
|
539 @param interval: another interval
|
|
|
540 @type interval: class L{Interval<Interval>}
|
|
|
541 @param normalization: whether the sum of the merge should be normalized wrt the number of mappings of each elements
|
|
|
542 @type normalization: boolean
|
|
|
543 """
|
|
|
544 if self.getChromosome() != interval.getChromosome():
|
|
|
545 raise Exception("Cannot merge '%s' and '%s' for they are on different chromosomes." % (str(self), str(interval)))
|
|
|
546 direction = None
|
|
|
547 if self.getStart() == self.getEnd():
|
|
|
548 direction = interval.getDirection()
|
|
|
549 elif interval.getStart() == interval.getEnd():
|
|
|
550 direction = self.getDirection()
|
|
|
551 elif self.getDirection() != interval.getDirection():
|
|
|
552 raise Exception("Cannot merge '%s' and '%s' for they are on different strands." % (str(self), str(interval)))
|
|
|
553 self.setStart(min(self.getStart(), interval.getStart()))
|
|
|
554 self.setEnd(max(self.getEnd(), interval.getEnd()))
|
|
|
555 if direction != None:
|
|
|
556 self.setDirection(direction)
|
|
|
557 nbElements = 0.0
|
|
|
558 for element in (self, interval):
|
|
|
559 for tagName in ("nbElements", "nbOccurrences"):
|
|
|
560 if tagName not in element.getTagNames():
|
|
|
561 element.setTagValue(tagName, 1)
|
|
|
562 nbElements += float(element.getTagValue("nbElements")) / float(element.getTagValue("nbOccurrences")) if normalization else float(element.getTagValue("nbElements"))
|
|
|
563 self.setTagValue("nbElements", nbElements)
|
|
|
564 self.bin = None
|
|
|
565 for tagName in ("identity", "nbOccurrences", "occurrence", "nbMismatches", "nbGaps", "rank", "evalue", "bestRegion"):
|
|
|
566 if tagName in self.getTagNames():
|
|
|
567 del self.tags[tagName]
|
|
|
568
|
|
|
569
|
|
|
570 def getBin(self):
|
|
|
571 """
|
|
|
572 Get the bin of the interval
|
|
|
573 Computed on the fly
|
|
|
574 """
|
|
|
575 if self.bin == None:
|
|
|
576 self.bin = getBin(self.getStart(), self.getEnd())
|
|
|
577 return self.bin
|
|
|
578
|
|
|
579
|
|
|
580 def getBins(self):
|
|
|
581 """
|
|
|
582 Get all the bin this interval could fall into
|
|
|
583 """
|
|
|
584 return getOverlappingBins(self.getStart(), self.getEnd())
|
|
|
585
|
|
|
586
|
|
|
587 def getSqlVariables(cls):
|
|
|
588 """
|
|
|
589 Get the properties of the object that should be saved in a database
|
|
|
590 """
|
|
|
591 variables = ["name", "chromosome", "start", "end", "direction", "tags", "bin"]
|
|
|
592 return variables
|
|
|
593 getSqlVariables = classmethod(getSqlVariables)
|
|
|
594
|
|
|
595
|
|
|
596 def setSqlValues(self, array):
|
|
|
597 """
|
|
|
598 Set the values of the properties of this object as given by a results line of a SQL query
|
|
|
599 """
|
|
|
600 self.id = array[0]
|
|
|
601 self.name = array[1].strip("'")
|
|
|
602 self.setChromosome(array[2].strip("'"))
|
|
|
603 self.setStart(array[3])
|
|
|
604 self.setEnd(array[4])
|
|
|
605 self.setDirection(array[5])
|
|
|
606 self.setTagValues(array[6].strip("'"), ";", "=")
|
|
|
607 self.bin = array[7]
|
|
|
608
|
|
|
609
|
|
|
610 def getSqlValues(self):
|
|
|
611 """
|
|
|
612 Get the values of the properties that should be saved in a database
|
|
|
613 """
|
|
|
614 values = dict()
|
|
|
615 values["name"] = self.name
|
|
|
616 values["chromosome"] = self.getChromosome()
|
|
|
617 values["start"] = self.getStart()
|
|
|
618 values["end"] = self.getEnd()
|
|
|
619 values["direction"] = self.getDirection()
|
|
|
620 values["tags"] = self.getTagValues(";", "=")
|
|
|
621 values["bin"] = self.getBin()
|
|
|
622 return values
|
|
|
623
|
|
|
624
|
|
|
625 def getSqlTypes(cls):
|
|
|
626 """
|
|
|
627 Get the values of the properties that should be saved in a database
|
|
|
628 """
|
|
|
629 types = dict()
|
|
|
630 types["name"] = "varchar"
|
|
|
631 types["chromosome"] = "varchar"
|
|
|
632 types["start"] = "int"
|
|
|
633 types["end"] = "int"
|
|
|
634 types["direction"] = "tinyint"
|
|
|
635 types["tags"] = "varchar"
|
|
|
636 types["bin"] = "int"
|
|
|
637 return types
|
|
|
638 getSqlTypes = classmethod(getSqlTypes)
|
|
|
639
|
|
|
640
|
|
|
641 def getSqlSizes(cls):
|
|
|
642 """
|
|
|
643 Get the sizes of the properties that should be saved in a database
|
|
|
644 """
|
|
|
645 sizes = dict()
|
|
|
646 sizes["name"] = 255
|
|
|
647 sizes["chromosome"] = 255
|
|
|
648 sizes["start"] = 11
|
|
|
649 sizes["end"] = 11
|
|
|
650 sizes["direction"] = 4
|
|
|
651 sizes["tags"] = 1023
|
|
|
652 sizes["bin"] = 11
|
|
|
653 return sizes
|
|
|
654 getSqlSizes = classmethod(getSqlSizes)
|
|
|
655
|
|
|
656
|
|
|
657 def printCoordinates(self):
|
|
|
658 """
|
|
|
659 Print start and end positions (depending on the direction of the interval)
|
|
|
660 """
|
|
|
661 if self.getDirection() == 1:
|
|
|
662 return "%d-%d" % (self.getStart(), self.getEnd())
|
|
|
663 else:
|
|
|
664 return "%d-%d" % (self.getEnd(), self.getStart())
|
|
|
665
|
|
|
666
|
|
|
667 def extractSequence(self, parser):
|
|
|
668 """
|
|
|
669 Get the sequence corresponding to this interval
|
|
|
670 @param parser: a parser to a FASTA file
|
|
|
671 @type parser: class L{SequenceListParser<SequenceListParser>}
|
|
|
672 @return : a instance of L{Sequence<Sequence>}
|
|
|
673 """
|
|
|
674 return parser.getSubSequence(self.getChromosome(), self.getStart(), self.getEnd(), self.getDirection(), self.name)
|
|
|
675
|
|
|
676
|
|
|
677 def extractWigData(self, parser):
|
|
|
678 """
|
|
|
679 Get the data retrieved from a wig file
|
|
|
680 @param parser: a parser class to a WIG file
|
|
|
681 @type parser: class L{WigParser<WigParser>}
|
|
|
682 """
|
|
|
683 data = parser.getRange(self.getChromosome(), self.getStart(), self.getEnd())
|
|
|
684 if self.getDirection() == -1:
|
|
|
685 if parser.strands:
|
|
|
686 newData = {}
|
|
|
687 for strand in data:
|
|
|
688 data[strand].reverse()
|
|
|
689 newData[-strand] = data[strand]
|
|
|
690 data = newData
|
|
|
691 else:
|
|
|
692 data.reverse()
|
|
|
693 return data
|
|
|
694
|
|
|
695
|
|
|
696 def __str__(self):
|
|
|
697 """
|
|
|
698 Output a simple representation of this interval
|
|
|
699 """
|
|
|
700 direction = "+"
|
|
|
701 if self.getDirection() == -1:
|
|
|
702 direction = "-"
|
|
|
703 string = "%s:%d-%d (%s)" % (self.getChromosome(), self.getStart(), self.getEnd(), direction)
|
|
|
704 if self.name != "":
|
|
|
705 string = "(%s) %s" % (self.name, string)
|
|
|
706 return string
|
|
|
707
|
