Mercurial > repos > yufei-luo > s_mart

comparison commons/core/writer/FastqWriter.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.SequenceListWriter import SequenceListWriter
31
32
33 class FastqWriter(SequenceListWriter):
34 """
35 A class that writes a sequence list into a file with FASTQ 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 super(FastqWriter, self).__init__(fileName, verbosity)
54
55
56 @staticmethod
57 def getFileFormats():
58 """
59 Get the format of the file
60 """
61 return ["fastq", "mfq"]
62
63
64 @staticmethod
65 def getExtension():
66 """
67 Get the usual extension for the file
68 """
69 return "fastq"
70
71
72 def getLine(self, sequence):
73 """
74 Convert a sequence
75 @param sequence: sequence to be written
76 @type sequence: class L{Sequence<Sequence>}
77 """
78 return sequence.printFastq()