|
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 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
|
