Mercurial > repos > yufei-luo > s_mart

comparison commons/core/writer/UcscWriter.py @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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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 from commons.core.writer.BedWriter import BedWriter
31
32 class UcscWriter(BedWriter):
33 """
34 A class that writes a transcript list into a file with UCSC BED format (minor differences with BED format)
35 """
36
37
38 def __init__(self, fileName, verbosity = 0):
39 """
40 Constructor
41 @param fileName: name of the file
42 @type fileName: string
43 @param verbosity: verbosity
44 @type verbosity: int
45 """
46 super(UcscWriter, self).__init__(fileName, verbosity)
47
48
49 @staticmethod
50 def getFileFormats():
51 """
52 Get the format of the file
53 """
54 return ["ucsc"]
55
56
57 @staticmethod
58 def getExtension():
59 """
60 Get the usual extension for the file
61 """
62 return "bed"
63
64
65 def printTranscript(self, transcript):
66 """
67 Export the given transcript with GBrowse format
68 @param transcript: transcript to be printed
69 @type transcript: class L{Transcript<Transcript>}
70 @return: a string
71 """
72 return transcript.printUcsc()
73