Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/writer/FastaWriter.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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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 FastaWriter(SequenceListWriter): | |
34 """ | |
35 A class that writes a sequence list into a file with FASTA 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(FastaWriter, self).__init__(fileName, verbosity) | |
54 | |
55 @staticmethod | |
56 def getFileFormats(): | |
57 """ | |
58 Get the format of the file | |
59 """ | |
60 return ["fasta", "mfa"] | |
61 | |
62 | |
63 @staticmethod | |
64 def getExtension(): | |
65 """ | |
66 Get the usual extension for the file | |
67 """ | |
68 return "fasta" | |
69 | |
70 | |
71 def getLine(self, sequence): | |
72 """ | |
73 Convert a sequence | |
74 @param sequence: sequence to be written | |
75 @type sequence: class L{Sequence<Sequence>} | |
76 """ | |
77 return sequence.printFasta() |