|
6
|
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
|
