Mercurial > repos > yufei-luo > s_mart

comparison commons/core/writer/SamWriter.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 import os
31 import random
32 from commons.core.writer.TranscriptListWriter import TranscriptListWriter
33
34
35 class SamWriter(TranscriptListWriter):
36 """
37 A class that writes a transcript list into a file with SAM format
38 @ivar sizes: estimated sizes of the chromosomes
39 @type sizes: dict of string to int
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 super(SamWriter, self).__init__(fileName, verbosity)
52 self.sizes = {}
53 self.headerWritten = False
54
55
56 def close(self):
57 """
58 Close file (trick to add header)
59 """
60 super(SamWriter, self).close()
61 if self.headerWritten:
62 return
63 tmpFileName = "tmpFile%d.sam" % (random.randint(0, 100000))
64 tmpHandle = open(tmpFileName, "w")
65 for chromosome, size in self.sizes.iteritems():
66 tmpHandle.write("@SQ\tSN:%s\tLN:%d\n" % (chromosome, size))
67 self.handle = open(self.fileName)
68 for line in self.handle:
69 tmpHandle.write(line)
70 tmpHandle.close()
71 self.handle.close()
72 os.rename(tmpFileName, self.fileName)
73 self.headerWritten = True
74
75
76 @staticmethod
77 def getFileFormats():
78 """
79 Get the format of the file
80 """
81 return ["sam"]
82
83
84 @staticmethod
85 def getExtension():
86 """
87 Get the usual extension for the file
88 """
89 return "sam"
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 self.sizes[transcript.getChromosome()] = max(transcript.getEnd(), self.sizes.get(transcript.getChromosome(), 0))
100 return transcript.printSam()
101