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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 """
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32 Clean a GFF file (as given by NCBI or TAIR) and outputs a GFF3 file.
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33 """
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34
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35 import os
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36 import re
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37 from optparse import OptionParser
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38 from commons.core.parsing.GffParser import *
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39 from SMART.Java.Python.misc.RPlotter import *
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40 from SMART.Java.Python.misc.Progress import Progress
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41 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
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42
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43 count = {}
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44
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45 class ParsedLine(object):
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40
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46 def __init__(self, line, cpt):
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47 self.line = line
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48 self.cpt = cpt
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49 self.parse()
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6
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50
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40
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51 def parse(self):
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52 self.line = self.line.strip()
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53 self.splittedLine = self.line.split(None, 8)
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54 if len(self.splittedLine) < 9:
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55 raise Exception("Line '%s' has less than 9 fields. Exiting..." % (self.line))
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56 self.type = self.splittedLine[2]
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57 self.parseOptions()
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58 self.getId()
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59 self.getParents()
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6
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60
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40
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61 def parseOptions(self):
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62 self.parsedOptions = {}
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63 for option in self.splittedLine[8].split(";"):
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64 option = option.strip()
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65 if option == "": continue
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66 posSpace = option.find(" ")
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67 posEqual = option.find("=")
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68 if posEqual != -1 and (posEqual < posSpace or posSpace == -1):
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69 key, value = option.split("=", 1)
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70 elif posSpace != -1:
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71 key, value = option.split(None, 1)
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72 else:
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73 key = "ID"
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74 value = option
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75 self.parsedOptions[key.strip()] = value.strip(" \"")
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6
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76
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40
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77 def getId(self):
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78 for key in self.parsedOptions:
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79 if key.lower() == "id":
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80 self.id = self.parsedOptions[key]
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81 return
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82 if "Parent" in self.parsedOptions:
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83 parent = self.parsedOptions["Parent"].split(",")[0]
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84 if parent not in count:
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85 count[parent] = {}
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86 if self.type not in count[parent]:
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87 count[parent][self.type] = 0
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88 count[parent][self.type] += 1
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89 self.id = "%s-%s-%d" % (parent, self.type, count[parent][self.type])
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90 else:
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91 self.id = "smart%d" % (self.cpt)
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92 self.parsedOptions["ID"] = self.id
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6
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93
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40
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94 def getParents(self):
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95 for key in self.parsedOptions:
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96 if key.lower() in ("parent", "derives_from"):
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97 self.parents = self.parsedOptions[key].split(",")
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98 return
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99 self.parents = None
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6
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100
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40
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101 def removeParent(self):
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102 for key in self.parsedOptions.keys():
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103 if key.lower() in ("parent", "derives_from"):
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104 del self.parsedOptions[key]
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6
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105
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40
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106 def export(self):
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107 self.splittedLine[8] = ";".join(["%s=%s" % (key, value) for key, value in self.parsedOptions.iteritems()])
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108 return "%s\n" % ("\t".join(self.splittedLine))
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6
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109
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110
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111 class CleanGff(object):
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112
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40
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113 def __init__(self, verbosity = 1):
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114 self.verbosity = verbosity
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115 self.lines = {}
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116 self.acceptedTypes = []
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117 self.parents = []
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118 self.children = {}
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6
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119
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40
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120 def setInputFileName(self, name):
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121 self.inputFile = open(name)
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122
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123 def setOutputFileName(self, name):
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124 self.outputFile = open(name, "w")
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125
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126 def setAcceptedTypes(self, types):
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127 self.acceptedTypes = types
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6
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128
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40
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129 def parse(self):
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130 progress = UnlimitedProgress(100000, "Reading input file", self.verbosity)
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131 for cpt, line in enumerate(self.inputFile):
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132 if not line or line[0] == "#": continue
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133 if line[0] == ">": break
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134 parsedLine = ParsedLine(line, cpt)
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135 if parsedLine.type in self.acceptedTypes:
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136 if parsedLine.id in self.lines:
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137 cpt = 1
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138 while "%s-%d" % (parsedLine.id, cpt) in self.lines:
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139 cpt += 1
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140 parsedLine.id = "%s-%d" % (parsedLine.id, cpt)
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141 self.lines[parsedLine.id] = parsedLine
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142 progress.inc()
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143 progress.done()
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6
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144
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40
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145 def sort(self):
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146 progress = Progress(len(self.lines.keys()), "Sorting file", self.verbosity)
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147 for line in self.lines.values():
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148 parentFound = False
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149 if line.parents:
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150 for parent in line.parents:
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151 if parent in self.lines:
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152 parentFound = True
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153 if parent in self.children:
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154 self.children[parent].append(line)
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155 else:
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156 self.children[parent] = [line]
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157 if not parentFound:
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158 line.removeParent()
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159 self.parents.append(line)
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160 progress.inc()
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161 progress.done()
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6
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162
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40
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163 def write(self):
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164 progress = Progress(len(self.parents), "Writing output file", self.verbosity)
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165 for line in self.parents:
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166 self.writeLine(line)
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167 progress.inc()
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168 self.outputFile.close()
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169 progress.done()
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6
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170
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40
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171 def writeLine(self, line):
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172 self.outputFile.write(line.export())
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173 if line.id in self.children:
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174 for child in self.children[line.id]:
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175 self.writeLine(child)
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6
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176
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40
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177 def run(self):
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178 self.parse()
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179 self.sort()
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180 self.write()
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6
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181
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182
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183 if __name__ == "__main__":
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40
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184
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185 # parse command line
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186 description = "Clean GFF v1.0.3: Clean a GFF file (as given by NCBI) and outputs a GFF3 file. [Category: Other]"
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6
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187
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188 parser = OptionParser(description = description)
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189 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file name [compulsory] [format: file in GFF format]")
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190 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
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191 parser.add_option("-t", "--types", dest="types", action="store", default="mRNA,exon", type="string", help="list of comma-separated types that you want to keep [format: string] [default: mRNA,exon]")
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192 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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193 (options, args) = parser.parse_args()
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6
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194
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40
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195 cleanGff = CleanGff(options.verbosity)
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196 cleanGff.setInputFileName(options.inputFileName)
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197 cleanGff.setOutputFileName(options.outputFileName)
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198 cleanGff.setAcceptedTypes(options.types.split(","))
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199 cleanGff.run()
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6
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200
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