Mercurial > repos > yufei-luo > s_mart
comparison commons/core/writer/TranscriptWriter.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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5:ea3082881bf8 | 6:769e306b7933 |
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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 import os | |
31 import sys | |
32 from commons.core.writer.WriterChooser import WriterChooser | |
33 from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter | |
34 | |
35 class TranscriptWriter(object): | |
36 """ | |
37 An interface class that writes a list of transcripts, handle different formats | |
38 @ivar container: container of the data | |
39 @type container: L{TranscriptContainer<TranscriptContainer>} | |
40 @ivar format: format of the data to be printed | |
41 @type format: string | |
42 @ivar file: the file where to print | |
43 @type file: string | |
44 @ivar type: type of the data (transcripts, mappings or mySQL) | |
45 @type type: string | |
46 @ivar writer: a transcript list writer | |
47 @type writer: L{TranscriptListWriter<TranscriptListWriter>} or None | |
48 @ivar mode: use a container or enter transcript one by one | |
49 @type mode: string | |
50 @ivar verbosity: verbosity | |
51 @type verbosity: int | |
52 """ | |
53 | |
54 def __init__(self, file, format, verbosity = 0): | |
55 """ | |
56 Constructor | |
57 @param container: container of the data | |
58 @type container: string | |
59 @param format: format of the data | |
60 @type format: string | |
61 @param file: file where to print | |
62 @type file: string | |
63 @param verbosity: verbosity | |
64 @type verbosity: int | |
65 """ | |
66 self.container = None | |
67 self.format = format | |
68 self.file = file | |
69 | |
70 self.verbosity = verbosity | |
71 self.type = None | |
72 self.writer = None | |
73 self.mode = None | |
74 if self.format == None: | |
75 sys.exit("Error! Writer input format is empty!") | |
76 | |
77 if self.format == "sql": | |
78 self.type = "sql" | |
79 pos = self.file.rfind(os.sep) | |
80 if pos > -1: | |
81 self.file = self.file[pos+1:] | |
82 self.writer = MySqlTranscriptWriter(self.file, self.verbosity) | |
83 else: | |
84 writerChooser = WriterChooser(self.verbosity) | |
85 writerChooser.findFormat(self.format) | |
86 self.writer = writerChooser.getWriter(self.file) | |
87 self.type = writerChooser.getType() | |
88 | |
89 | |
90 def close(self): | |
91 """ | |
92 Close writer | |
93 """ | |
94 if self.writer != None: | |
95 self.writer.close() | |
96 | |
97 | |
98 def setContainer(self, container): | |
99 """ | |
100 Set a container for the data | |
101 @param container: container of the data | |
102 @type container: class L{TranscriptContainer<TranscriptContainer>} | |
103 """ | |
104 self.container = container | |
105 if self.mode == "transcript": | |
106 raise Exception("Error! TranscriptWriter '%s' on 'transcript' mode is currently used on 'container' mode." % (self.file)) | |
107 self.mode = "container" | |
108 | |
109 | |
110 def addTranscript(self, transcript): | |
111 """ | |
112 Add a transcript to write | |
113 @param transcript: a transcript | |
114 @type transcript: class L{Transcript<Transcript>} | |
115 """ | |
116 self.writer.addTranscript(transcript) | |
117 if self.mode == "container": | |
118 sys.exit("Error! TranscriptWriter '%s' on 'container' mode is currently used on 'transcript' mode." % (self.file)) | |
119 self.mode = "transcript" | |
120 | |
121 | |
122 def addElement(self, transcript): | |
123 """ | |
124 Same as addTranscript | |
125 """ | |
126 self.addTranscript(transcript) | |
127 | |
128 | |
129 def setTitle(self, title): | |
130 """ | |
131 Possibly write a title for the list | |
132 @param title: a title for the list | |
133 @type title: string | |
134 """ | |
135 if self.writer != None: | |
136 self.writer.setTitle(title) | |
137 | |
138 def setFeature(self, feature): | |
139 """ | |
140 Possibly Set the name of the feature | |
141 @param title: the title of the feature | |
142 @type feature: string | |
143 """ | |
144 if self.writer != None: | |
145 self.writer.setFeature(feature) | |
146 | |
147 def setFeaturePart(self, featurePart): | |
148 """ | |
149 Possibly Set the name of the feature part | |
150 @param title: the title of the feature part | |
151 @type featurePart: string | |
152 """ | |
153 if self.writer != None: | |
154 self.writer.setFeaturePart(featurePart) | |
155 | |
156 def setStrands(self, strands): | |
157 """ | |
158 Possibly consider both strands separately | |
159 @param strands: whether both strands should be considered separately | |
160 @type strands: boolean | |
161 """ | |
162 if self.writer != None: | |
163 self.writer.setStrands(strands) | |
164 | |
165 | |
166 def write(self): | |
167 """ | |
168 Write the content and possibly convert data | |
169 """ | |
170 if self.type == "transcript" or self.type == "sequence": | |
171 if self.mode == "container": | |
172 self.writer.addTranscriptList(self.container) | |
173 return | |
174 | |
175 if self.mode == "transcript" or self.type == "sequence": | |
176 self.writer.write() | |
177 return | |
178 | |
179 if self.container.format != "sql": | |
180 self.container.storeIntoDatabase() | |
181 tables = self.container.getTables() | |
182 for chromosome in tables: | |
183 tables[chromosome].rename("%s_%s" % (self.file, chromosome)) | |
184 return | |
185 | |
186 | |
187 def addSequenceFile(self, fileName): | |
188 self.writer.addSequenceFile(fileName) | |
189 |