Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/cleaning/TranscriptListCleaner.py @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
parents 769e306b7933
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35:d94018ca4ada 36:44d5973c188c
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 sys
31 from SMART.Java.Python.structure.TranscriptList import TranscriptList
32 from SMART.Java.Python.misc.Progress import Progress
33 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
34
35 class TranscriptListCleaner(object):
36 """A (quite generic) class that cleans a file containing transcripts"""
37
38 def __init__(self, verbosity = 0):
39 self.verbosity = verbosity
40
41 def setInputFileName(self, fileName):
42 try:
43 self.inputHandle = open(fileName)
44 except IOError:
45 raise Exception("Error! Transcript file '%s' does not exist! Exiting..." % (self.fileName))
46
47 def setOutputFileName(self, fileName):
48 try:
49 self.outputHandle = open(fileName, "w")
50 except IOError:
51 raise Exception("Error! Transcript file '%s' does not exist! Exiting..." % (self.fileName))
52
53 def getFileFormats():
54 pass
55 getFileFormats = staticmethod(getFileFormats)
56
57 def close(self):
58 self.inputHandle.close()
59 self.outputHandle.close()
60
61 def clean(self):
62 self._clean()
63 self.close()