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comparison smart_toolShed/SMART/Java/Python/cleanGff.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
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