Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/cleaning/GffCleaner.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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 from SMART.Java.Python.cleaning.TranscriptListCleaner import TranscriptListCleaner
36 from SMART.Java.Python.misc.Progress import Progress
37 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
38
39 count = {}
40
41 class ParsedLine(object):
42 def __init__(self, line, cpt):
43 self.line = line
44 self.cpt = cpt
45 self.parse()
46
47 def parse(self):
48 self.line = self.line.strip()
49 self.splittedLine = self.line.split(None, 8)
50 if len(self.splittedLine) < 9:
51 raise Exception("Line '%s' has less than 9 fields. Exiting..." % (self.line))
52 self.type = self.splittedLine[2]
53 self.parseOptions()
54 self.getId()
55 self.getParents()
56
57 def parseOptions(self):
58 self.parsedOptions = {}
59 for option in self.splittedLine[8].split(";"):
60 option = option.strip()
61 if option == "": continue
62 posSpace = option.find(" ")
63 posEqual = option.find("=")
64 if posEqual != -1 and (posEqual < posSpace or posSpace == -1):
65 key, value = option.split("=", 1)
66 elif posSpace != -1:
67 key, value = option.split(None, 1)
68 else:
69 key = "ID"
70 value = option
71 self.parsedOptions[key.strip()] = value.strip(" \"")
72
73 def getId(self):
74 for key in self.parsedOptions:
75 if key.lower() == "id":
76 self.id = self.parsedOptions[key]
77 return
78 if "Parent" in self.parsedOptions:
79 parent = self.parsedOptions["Parent"].split(",")[0]
80 if parent not in count:
81 count[parent] = {}
82 if self.type not in count[parent]:
83 count[parent][self.type] = 0
84 count[parent][self.type] += 1
85 self.id = "%s-%s-%d" % (parent, self.type, count[parent][self.type])
86 else:
87 self.id = "smart%d" % (self.cpt)
88 self.parsedOptions["ID"] = self.id
89
90 def getParents(self):
91 for key in self.parsedOptions:
92 if key.lower() in ("parent", "derives_from"):
93 self.parents = self.parsedOptions[key].split(",")
94 return
95 self.parents = None
96
97 def removeParent(self):
98 for key in self.parsedOptions.keys():
99 if key.lower() in ("parent", "derives_from"):
100 del self.parsedOptions[key]
101
102 def export(self):
103 self.splittedLine[8] = ";".join(["%s=%s" % (key, value) for key, value in self.parsedOptions.iteritems()])
104 return "%s\n" % ("\t".join(self.splittedLine))
105
106
107 class GffCleaner(TranscriptListCleaner):
108
109 def __init__(self, verbosity = 1):
110 super(GffCleaner, self).__init__(verbosity)
111 self.lines = {}
112 self.acceptedTypes = ["mRNA", "transcript", "exon"]
113 self.parents = []
114 self.children = {}
115
116 def getFileFormats():
117 return ["gff", "gff2", "gff3"]
118 getFileFormats = staticmethod(getFileFormats)
119
120 def setAcceptedTypes(self, types):
121 self.acceptedTypes = types
122
123 def parse(self):
124 progress = UnlimitedProgress(100000, "Reading input file", self.verbosity)
125 for cpt, line in enumerate(self.inputHandle):
126 if not line or line[0] == "#": continue
127 if line[0] == ">": break
128 parsedLine = ParsedLine(line, cpt)
129 if self.acceptedTypes == None or parsedLine.type in self.acceptedTypes:
130 self.lines[parsedLine.id] = parsedLine
131 progress.inc()
132 progress.done()
133
134 def sort(self):
135 progress = Progress(len(self.lines.keys()), "Sorting file", self.verbosity)
136 for line in self.lines.values():
137 parentFound = False
138 if line.parents:
139 for parent in line.parents:
140 if parent in self.lines:
141 parentFound = True
142 if parent in self.children:
143 self.children[parent].append(line)
144 else:
145 self.children[parent] = [line]
146 if not parentFound:
147 line.removeParent()
148 self.parents.append(line)
149 progress.inc()
150 progress.done()
151
152 def write(self):
153 progress = Progress(len(self.parents), "Writing output file", self.verbosity)
154 for line in self.parents:
155 self.writeLine(line)
156 progress.inc()
157 progress.done()
158
159 def writeLine(self, line):
160 self.outputHandle.write(line.export())
161 if line.id in self.children:
162 for child in self.children[line.id]:
163 self.writeLine(child)
164
165 def _clean(self):
166 self.parse()
167 self.sort()
168 self.write()