6
+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2010
+ − 4 #
+ − 5 # This software is governed by the CeCILL license under French law and
+ − 6 # abiding by the rules of distribution of free software. You can use,
+ − 7 # modify and/ or redistribute the software under the terms of the CeCILL
+ − 8 # license as circulated by CEA, CNRS and INRIA at the following URL
+ − 9 # "http://www.cecill.info".
+ − 10 #
+ − 11 # As a counterpart to the access to the source code and rights to copy,
+ − 12 # modify and redistribute granted by the license, users are provided only
+ − 13 # with a limited warranty and the software's author, the holder of the
+ − 14 # economic rights, and the successive licensors have only limited
+ − 15 # liability.
+ − 16 #
+ − 17 # In this respect, the user's attention is drawn to the risks associated
+ − 18 # with loading, using, modifying and/or developing or reproducing the
+ − 19 # software by the user in light of its specific status of free software,
+ − 20 # that may mean that it is complicated to manipulate, and that also
+ − 21 # therefore means that it is reserved for developers and experienced
+ − 22 # professionals having in-depth computer knowledge. Users are therefore
+ − 23 # encouraged to load and test the software's suitability as regards their
+ − 24 # requirements in conditions enabling the security of their systems and/or
+ − 25 # data to be ensured and, more generally, to use and operate it in the
+ − 26 # same conditions as regards security.
+ − 27 #
+ − 28 # The fact that you are presently reading this means that you have had
+ − 29 # knowledge of the CeCILL license and that you accept its terms.
+ − 30 #
+ − 31 """
+ − 32 Clean a GFF file (as given by NCBI or TAIR) and outputs a GFF3 file.
+ − 33 """
+ − 34
+ − 35 import os
+ − 36 import re
+ − 37 from optparse import OptionParser
+ − 38 from commons.core.parsing.GffParser import *
+ − 39 from SMART.Java.Python.misc.RPlotter import *
+ − 40 from SMART.Java.Python.misc.Progress import Progress
+ − 41 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+ − 42
+ − 43 count = {}
+ − 44
+ − 45 class ParsedLine(object):
+ − 46 def __init__(self, line, cpt):
+ − 47 self.line = line
+ − 48 self.cpt = cpt
+ − 49 self.parse()
+ − 50
+ − 51 def parse(self):
+ − 52 self.line = self.line.strip()
+ − 53 self.splittedLine = self.line.split(None, 8)
+ − 54 if len(self.splittedLine) < 9:
+ − 55 raise Exception("Line '%s' has less than 9 fields. Exiting..." % (self.line))
+ − 56 self.type = self.splittedLine[2]
+ − 57 self.parseOptions()
+ − 58 self.getId()
+ − 59 self.getParents()
+ − 60
+ − 61 def parseOptions(self):
+ − 62 self.parsedOptions = {}
+ − 63 for option in self.splittedLine[8].split(";"):
+ − 64 option = option.strip()
+ − 65 if option == "": continue
+ − 66 posSpace = option.find(" ")
+ − 67 posEqual = option.find("=")
+ − 68 if posEqual != -1 and (posEqual < posSpace or posSpace == -1):
+ − 69 key, value = option.split("=", 1)
+ − 70 elif posSpace != -1:
+ − 71 key, value = option.split(None, 1)
+ − 72 else:
+ − 73 key = "ID"
+ − 74 value = option
+ − 75 self.parsedOptions[key.strip()] = value.strip(" \"")
+ − 76
+ − 77 def getId(self):
+ − 78 for key in self.parsedOptions:
+ − 79 if key.lower() == "id":
+ − 80 self.id = self.parsedOptions[key]
+ − 81 return
+ − 82 if "Parent" in self.parsedOptions:
+ − 83 parent = self.parsedOptions["Parent"].split(",")[0]
+ − 84 if parent not in count:
+ − 85 count[parent] = {}
+ − 86 if self.type not in count[parent]:
+ − 87 count[parent][self.type] = 0
+ − 88 count[parent][self.type] += 1
+ − 89 self.id = "%s-%s-%d" % (parent, self.type, count[parent][self.type])
+ − 90 else:
+ − 91 self.id = "smart%d" % (self.cpt)
+ − 92 self.parsedOptions["ID"] = self.id
+ − 93
+ − 94 def getParents(self):
+ − 95 for key in self.parsedOptions:
+ − 96 if key.lower() in ("parent", "derives_from"):
+ − 97 self.parents = self.parsedOptions[key].split(",")
+ − 98 return
+ − 99 self.parents = None
+ − 100
+ − 101 def removeParent(self):
+ − 102 for key in self.parsedOptions.keys():
+ − 103 if key.lower() in ("parent", "derives_from"):
+ − 104 del self.parsedOptions[key]
+ − 105
+ − 106 def export(self):
+ − 107 self.splittedLine[8] = ";".join(["%s=%s" % (key, value) for key, value in self.parsedOptions.iteritems()])
+ − 108 return "%s\n" % ("\t".join(self.splittedLine))
+ − 109
+ − 110
+ − 111 class CleanGff(object):
+ − 112
+ − 113 def __init__(self, verbosity = 1):
+ − 114 self.verbosity = verbosity
+ − 115 self.lines = {}
+ − 116 self.acceptedTypes = []
+ − 117 self.parents = []
+ − 118 self.children = {}
+ − 119
+ − 120 def setInputFileName(self, name):
+ − 121 self.inputFile = open(name)
+ − 122
+ − 123 def setOutputFileName(self, name):
+ − 124 self.outputFile = open(name, "w")
+ − 125
+ − 126 def setAcceptedTypes(self, types):
+ − 127 self.acceptedTypes = types
+ − 128
+ − 129 def parse(self):
+ − 130 progress = UnlimitedProgress(100000, "Reading input file", self.verbosity)
+ − 131 for cpt, line in enumerate(self.inputFile):
+ − 132 if not line or line[0] == "#": continue
+ − 133 if line[0] == ">": break
+ − 134 parsedLine = ParsedLine(line, cpt)
+ − 135 if parsedLine.type in self.acceptedTypes:
+ − 136 self.lines[parsedLine.id] = parsedLine
+ − 137 progress.inc()
+ − 138 progress.done()
+ − 139
+ − 140 def sort(self):
+ − 141 progress = Progress(len(self.lines.keys()), "Sorting file", self.verbosity)
+ − 142 for line in self.lines.values():
+ − 143 parentFound = False
+ − 144 if line.parents:
+ − 145 for parent in line.parents:
+ − 146 if parent in self.lines:
+ − 147 parentFound = True
+ − 148 if parent in self.children:
+ − 149 self.children[parent].append(line)
+ − 150 else:
+ − 151 self.children[parent] = [line]
+ − 152 if not parentFound:
+ − 153 line.removeParent()
+ − 154 self.parents.append(line)
+ − 155 progress.inc()
+ − 156 progress.done()
+ − 157
+ − 158 def write(self):
+ − 159 progress = Progress(len(self.parents), "Writing output file", self.verbosity)
+ − 160 for line in self.parents:
+ − 161 self.writeLine(line)
+ − 162 progress.inc()
+ − 163 self.outputFile.close()
+ − 164 progress.done()
+ − 165
+ − 166 def writeLine(self, line):
+ − 167 self.outputFile.write(line.export())
+ − 168 if line.id in self.children:
+ − 169 for child in self.children[line.id]:
+ − 170 self.writeLine(child)
+ − 171
+ − 172 def run(self):
+ − 173 self.parse()
+ − 174 self.sort()
+ − 175 self.write()
+ − 176
+ − 177
+ − 178 if __name__ == "__main__":
+ − 179
+ − 180 # parse command line
+ − 181 description = "Clean GFF v1.0.3: Clean a GFF file (as given by NCBI) and outputs a GFF3 file. [Category: Other]"
+ − 182
+ − 183 parser = OptionParser(description = description)
+ − 184 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file name [compulsory] [format: file in GFF format]")
+ − 185 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 186 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]")
+ − 187 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 188 (options, args) = parser.parse_args()
+ − 189
+ − 190 cleanGff = CleanGff(options.verbosity)
+ − 191 cleanGff.setInputFileName(options.inputFileName)
+ − 192 cleanGff.setOutputFileName(options.outputFileName)
+ − 193 cleanGff.setAcceptedTypes(options.types.split(","))
+ − 194 cleanGff.run()
+ − 195
