Mercurial > repos > yufei-luo > s_mart

comparison commons/core/writer/BedWriter.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 #
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.TranscriptListWriter import TranscriptListWriter
31
32
33 class BedWriter(TranscriptListWriter):
34 """
35 A class that writes a transcript list into a file with BED format
36 @ivar fileName: name of the file
37 @type fileName: string
38 @ivar handle: handle to the file
39 @type handle: file handle
40 @ivar header: first lines of the file
41 @type header: string
42 """
43
44
45 def __init__(self, fileName, verbosity = 0):
46 """
47 Constructor
48 @param fileName: name of the file
49 @type fileName: string
50 @param verbosity: verbosity
51 @type verbosity: int
52 """
53 self.header = "track name=reads description=\"Reads\" useScore=0 visibility=full offset=0\n"
54 super(BedWriter, self).__init__(fileName, verbosity)
55
56
57 @staticmethod
58 def getFileFormats():
59 """
60 Get the format of the file
61 """
62 return ["bed"]
63
64
65 @staticmethod
66 def getExtension():
67 """
68 Get the usual extension for the file
69 """
70 return "bed"
71
72
73 def setTitle(self, title):
74 """
75 Set the title of the track
76 @param title: the title of the track
77 @type title: string
78 """
79 if title != None:
80 self.header = "track name=%s description=\"%s\" useScore=0 visibility=full offset=0\n" % (title, title)
81
82
83 def copyProperties(self, bedParser):
84 """
85 Copy the properties collected by a parser, to produce a similar output
86 @param bedParser: a BED Parser parser
87 @type bedParser: class L{BedParser<BedParser>}
88 """
89 self.setTitle(bedParser.title)
90
91
92 def printTranscript(self, transcript):
93 """
94 Export the given transcript with GBrowse format
95 @param transcript: transcript to be printed
96 @type transcript: class L{Transcript<Transcript>}
97 @return: a string
98 """
99 return transcript.printBed()
100