|
6
|
1 #
|
|
|
2 # Copyright INRA-URGI 2009-2010
|
|
|
3 #
|
|
|
4 # This software is governed by the CeCILL license under French law and
|
|
|
5 # abiding by the rules of distribution of free software. You can use,
|
|
|
6 # modify and/ or redistribute the software under the terms of the CeCILL
|
|
|
7 # license as circulated by CEA, CNRS and INRIA at the following URL
|
|
|
8 # "http://www.cecill.info".
|
|
|
9 #
|
|
|
10 # As a counterpart to the access to the source code and rights to copy,
|
|
|
11 # modify and redistribute granted by the license, users are provided only
|
|
|
12 # with a limited warranty and the software's author, the holder of the
|
|
|
13 # economic rights, and the successive licensors have only limited
|
|
|
14 # liability.
|
|
|
15 #
|
|
|
16 # In this respect, the user's attention is drawn to the risks associated
|
|
|
17 # with loading, using, modifying and/or developing or reproducing the
|
|
|
18 # software by the user in light of its specific status of free software,
|
|
|
19 # that may mean that it is complicated to manipulate, and that also
|
|
|
20 # therefore means that it is reserved for developers and experienced
|
|
|
21 # professionals having in-depth computer knowledge. Users are therefore
|
|
|
22 # encouraged to load and test the software's suitability as regards their
|
|
|
23 # requirements in conditions enabling the security of their systems and/or
|
|
|
24 # data to be ensured and, more generally, to use and operate it in the
|
|
|
25 # same conditions as regards security.
|
|
|
26 #
|
|
|
27 # The fact that you are presently reading this means that you have had
|
|
|
28 # knowledge of the CeCILL license and that you accept its terms.
|
|
|
29 #
|
|
|
30 import re
|
|
|
31 import sys
|
|
|
32 try:
|
|
|
33 import cPickle as pickle
|
|
|
34 except:
|
|
|
35 import pickle
|
|
|
36 from SMART.Java.Python.structure.Interval import Interval
|
|
|
37 from commons.core.parsing.TranscriptListParser import TranscriptListParser
|
|
|
38 from SMART.Java.Python.structure.Transcript import Transcript
|
|
|
39
|
|
|
40
|
|
|
41 class PklParser(TranscriptListParser):
|
|
|
42 """A class that parses the intern PKL file and create a transcript list"""
|
|
|
43
|
|
|
44 def __init__(self, fileName, verbosity = 1):
|
|
|
45 self.title = None
|
|
|
46 super(PklParser, self).__init__(fileName, verbosity)
|
|
|
47 self.handle = open(fileName, "rb")
|
|
|
48 self.verbosity = verbosity
|
|
|
49 self.initAddress = 0
|
|
|
50 self.address = self.initAddress
|
|
|
51 self.over = False
|
|
|
52 self.chromosome = None
|
|
|
53
|
|
|
54 def __del__(self):
|
|
|
55 super(PklParser, self).__del__()
|
|
|
56
|
|
|
57 def getFileFormats():
|
|
|
58 return ["pkl"]
|
|
|
59 getFileFormats = staticmethod(getFileFormats)
|
|
|
60
|
|
|
61
|
|
|
62 def skipFirstLines(self):
|
|
|
63 return
|
|
|
64
|
|
|
65
|
|
|
66 def reset(self):
|
|
|
67 self.handle.seek(0)
|
|
|
68 self.initAddress = 0
|
|
|
69
|
|
|
70
|
|
|
71 def setChromosome(self, chromosome):
|
|
|
72 self.chromosome = chromosome
|
|
|
73
|
|
|
74
|
|
|
75 def gotoAddress(self, address):
|
|
|
76 self.handle.seek(address)
|
|
|
77 self.address = address
|
|
|
78
|
|
|
79
|
|
|
80 def getNextTranscript(self):
|
|
|
81 self.address = self.handle.tell()
|
|
|
82 try:
|
|
|
83 transcript = pickle.load(self.handle)
|
|
|
84 if self.chromosome != None and transcript.getChromosome() != self.chromosome:
|
|
|
85 self.over = True
|
|
|
86 return False
|
|
|
87 return transcript
|
|
|
88 except EOFError:
|
|
|
89 self.over = True
|
|
|
90 return False
|
|
|
91
|
|
|
92
|
|
|
93 def getIterator(self):
|
|
|
94 self.gotoAddress(self.initAddress)
|
|
|
95 while True:
|
|
|
96 transcript = self.getNextTranscript()
|
|
|
97 if not transcript:
|
|
|
98 self.over = True
|
|
|
99 return
|
|
|
100 yield transcript
|
|
|
101
|
|
|
102
|
|
|
103 def setInitAddress(self, address):
|
|
|
104 self.initAddress = address
|
|
|
105
|
|
|
106
|
|
|
107 def getCurrentTranscriptAddress(self):
|
|
|
108 return self.address
|
|
|
109
|
|
|
110
|
|
|
111 def isOver(self):
|
|
|
112 return self.over
|
