Mercurial > repos > yufei-luo > s_mart

comparison commons/core/writer/EmblWriter.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 EmblWriter(TranscriptListWriter):
34 """
35 A class that writes a transcript list into several files with EMBL 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 """
41
42
43 def __init__(self, fileName, verbosity = 0):
44 """
45 Constructor
46 @param fileName: name of the file
47 @type fileName: string
48 @param verbosity: verbosity
49 @type verbosity: int
50 """
51 self.fileName = fileName
52 self.verbosity = verbosity
53 self.handles = {}
54 self.handle = None
55
56
57 def __del__(self):
58 """
59 Destructor
60 Trick to append the sequences at the end of the EMBL files
61 """
62 handle = open(self.sequenceFileName)
63 currentHandle = None
64 for line in handle:
65 if line[0] == ">":
66 chromosome = line[1:].strip()
67 if chromosome in self.handles:
68 currentHandle = self.handles[chromosome]
69 else:
70 currentHandle = None
71 else:
72 if currentHandle != None:
73 currentHandle.write(line)
74 handle.close()
75 for handle in self.handles.values():
76 handle.close()
77
78
79 @staticmethod
80 def getFileFormats():
81 """
82 Get the format of the file
83 """
84 return ["embl"]
85
86
87 @staticmethod
88 def getExtension():
89 """
90 Get the usual extension for the file
91 """
92 return "embl"
93
94
95 def addTranscript(self, transcript):
96 """
97 Add a transcript to the list of transcripts to be written
98 @param transcript: transcript to be written
99 @type transcript: class L{Transcript<Transcript>}
100 """
101 chromosome = transcript.getChromosome()
102 if chromosome not in self.handles:
103 self.handles[chromosome] = open("%s%s.embl" % (self.fileName[:-len(".embl")], chromosome.title()), "w")
104 self.handles[chromosome].write(self.printTranscript(transcript))
105
106
107 def printTranscript(self, transcript):
108 """
109 Export the given transcript with GFF2 format
110 @param transcript: transcript to be printed
111 @type transcript: class L{Transcript<Transcript>}
112 @return: a string
113 """
114 return transcript.printEmbl()
115
116