Mercurial > repos > yufei-luo > s_mart
comparison commons/core/writer/CsvWriter.py @ 36:44d5973c188c
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author | m-zytnicki |
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date | Tue, 30 Apr 2013 15:02:29 -0400 |
parents | 769e306b7933 |
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35:d94018ca4ada | 36:44d5973c188c |
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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 random | |
32 from commons.core.writer.TranscriptListWriter import TranscriptListWriter | |
33 from SMART.Java.Python.misc.Progress import Progress | |
34 | |
35 class CsvWriter(TranscriptListWriter): | |
36 """ | |
37 A class that writes a transcript list into a file with CSV (Excel) format | |
38 @ivar fileName: name of the file | |
39 @type fileName: string | |
40 @ivar handle: handle to the file | |
41 @type handle: file handle | |
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(CsvWriter, self).__init__(fileName, verbosity) | |
54 self.header = "" | |
55 self.title = "chromosome,start,end,strand,exons,tags\n" | |
56 self.modified = False | |
57 | |
58 | |
59 def __del__(self): | |
60 """ | |
61 Destructor | |
62 (Trick to write 1 tag per column) | |
63 """ | |
64 if self.handle != None: | |
65 self.modifyCsv() | |
66 super(CsvWriter, self).__del__() | |
67 | |
68 | |
69 def close(self): | |
70 if self.handle != None: | |
71 self.modifyCsv() | |
72 super(CsvWriter, self).close() | |
73 | |
74 | |
75 def modifyCsv(self): | |
76 """ | |
77 Clean CSV file so that there is one column per tag | |
78 """ | |
79 if self.modified: | |
80 return | |
81 | |
82 # read all the tags | |
83 self.handle.close() | |
84 self.handle = open(self.fileName) | |
85 nbFirstFields = 5 | |
86 tags = set() | |
87 if self.verbosity >= 10: | |
88 print "Modifying CSV file..." | |
89 number = -1 | |
90 for number, line in enumerate(self.handle): | |
91 if number != 0: | |
92 theseTags = line.strip().split(",")[nbFirstFields:] | |
93 for tag in theseTags: | |
94 if tag.find("=") != -1: | |
95 (key, value) = tag.split("=", 1) | |
96 if value != None: | |
97 tags.add(key) | |
98 if self.verbosity >= 10: | |
99 print " ...done" | |
100 | |
101 # re-write the file | |
102 tmpFileName = "tmpFile%d.csv" % (random.randint(0, 100000)) | |
103 tmpFile = open(tmpFileName, "w") | |
104 self.handle.seek(0) | |
105 progress = Progress(number + 1, "Re-writting CSV file", self.verbosity) | |
106 tmpFile.write(self.title.replace("tags", ",".join(sorted(tags)))) | |
107 for line in self.handle: | |
108 tagValues = dict([(key, None) for key in tags]) | |
109 tmpFile.write(",".join(line.strip().split(",")[:nbFirstFields])) | |
110 for tag in line.strip().split(",")[nbFirstFields:]: | |
111 if tag.find("=") != -1: | |
112 key = tag.split("=", 1)[0] | |
113 tagValues[key] = tag.split("=", 1)[1] | |
114 else: | |
115 tagValues[key] += ";%s" % (tag) | |
116 for key in sorted(tagValues.keys()): | |
117 tmpFile.write(",%s" % (tagValues[key])) | |
118 tmpFile.write("\n") | |
119 progress.inc() | |
120 tmpFile.close() | |
121 | |
122 # replace former file | |
123 import shutil | |
124 shutil.move(tmpFile.name, self.fileName) | |
125 progress.done() | |
126 self.modified = True | |
127 | |
128 | |
129 @staticmethod | |
130 def getFileFormats(): | |
131 """ | |
132 Get the format of the file | |
133 """ | |
134 return ["csv", "xls", "excel"] | |
135 | |
136 | |
137 @staticmethod | |
138 def getExtension(): | |
139 """ | |
140 Get the usual extension for the file | |
141 """ | |
142 return "csv" | |
143 | |
144 | |
145 def printTranscript(self, transcript): | |
146 """ | |
147 Export the given transcript with GFF2 format | |
148 @param transcript: transcript to be printed | |
149 @type transcript: class L{Transcript<Transcript>} | |
150 @return: a string | |
151 """ | |
152 return transcript.printCsv() | |
153 |