Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/restrictSequenceList.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 #! /usr/bin/env python | |
2 # | |
3 # Copyright INRA-URGI 2009-2010 | |
4 # | |
5 # This software is governed by the CeCILL license under French law and | |
6 # abiding by the rules of distribution of free software. You can use, | |
7 # modify and/ or redistribute the software under the terms of the CeCILL | |
8 # license as circulated by CEA, CNRS and INRIA at the following URL | |
9 # "http://www.cecill.info". | |
10 # | |
11 # As a counterpart to the access to the source code and rights to copy, | |
12 # modify and redistribute granted by the license, users are provided only | |
13 # with a limited warranty and the software's author, the holder of the | |
14 # economic rights, and the successive licensors have only limited | |
15 # liability. | |
16 # | |
17 # In this respect, the user's attention is drawn to the risks associated | |
18 # with loading, using, modifying and/or developing or reproducing the | |
19 # software by the user in light of its specific status of free software, | |
20 # that may mean that it is complicated to manipulate, and that also | |
21 # therefore means that it is reserved for developers and experienced | |
22 # professionals having in-depth computer knowledge. Users are therefore | |
23 # encouraged to load and test the software's suitability as regards their | |
24 # requirements in conditions enabling the security of their systems and/or | |
25 # data to be ensured and, more generally, to use and operate it in the | |
26 # same conditions as regards security. | |
27 # | |
28 # The fact that you are presently reading this means that you have had | |
29 # knowledge of the CeCILL license and that you accept its terms. | |
30 # | |
31 """Restrict a sequence list with some names""" | |
32 | |
33 from optparse import OptionParser | |
34 from commons.core.parsing.ParserChooser import ParserChooser | |
35 from commons.core.writer.WriterChooser import WriterChooser | |
36 from SMART.Java.Python.misc.Progress import Progress | |
37 from SMART.Java.Python.misc import Utils | |
38 | |
39 class RestrictSequenceList(object): | |
40 | |
41 def __init__(self, verbosity): | |
42 self.verbosity = verbosity | |
43 self.exclude = False | |
44 | |
45 def setInputFileName(self, fileName, format): | |
46 chooser = ParserChooser(self.verbosity) | |
47 chooser.findFormat(format) | |
48 self.parser = chooser.getParser(fileName) | |
49 | |
50 def setExclusion(self, boolean): | |
51 self.exclude = boolean | |
52 | |
53 def setOutputFileName(self, fileName, format): | |
54 chooser = WriterChooser(self.verbosity) | |
55 chooser.findFormat(format) | |
56 self.writer = chooser.getWriter(fileName) | |
57 | |
58 def setNamesFileName(self, fileName): | |
59 self.namesFileName = fileName | |
60 | |
61 def _readNames(self): | |
62 self.names = [] | |
63 handle = open(self.namesFileName) | |
64 for name in handle: | |
65 self.names.append(name.strip()) | |
66 handle.close() | |
67 | |
68 def _write(self): | |
69 nbElements = self.parser.getNbItems() | |
70 progress = Progress(nbElements, "Parsing input file", self.verbosity) | |
71 nbRead = 0 | |
72 nbWritten = 0 | |
73 for element in self.parser.getIterator(): | |
74 name = element.getName() | |
75 nbRead += 1 | |
76 if Utils.xor(name in self.names, self.exclude): | |
77 self.writer.addElement(element) | |
78 nbWritten += 1 | |
79 if name in self.names: | |
80 self.names.remove(name) | |
81 progress.inc() | |
82 progress.done() | |
83 if self.verbosity > 0: | |
84 print "%d read" % (nbRead) | |
85 print "%d written (%d%%)" % (nbWritten, 0 if nbRead == 0 else round(float(nbWritten) / nbRead * 100)) | |
86 | |
87 def run(self): | |
88 self._readNames() | |
89 self._write() | |
90 if self.names: | |
91 print "Some names are not present in the file: %s" % ", ".join(self.names) | |
92 | |
93 | |
94 | |
95 if __name__ == "__main__": | |
96 | |
97 description = "Restrict Sequence List v1.0.1: Keep the elements of a list of sequences whose name is mentionned in a given file. [Category: Data Selection]" | |
98 | |
99 parser = OptionParser(description = description) | |
100 parser.add_option("-i", "--input", dest="inputFile", action="store", type="string", help="input file [compulsory] [format: file in sequence format given by -f]") | |
101 parser.add_option("-f", "--format", dest="format", action="store", default="fasta", type="string", help="format of the input and output files [compulsory] [format: sequence file format] [default: fasta]") | |
102 parser.add_option("-n", "--name", dest="names", action="store", type="string", help="names of the transcripts [compulsory] [format: file in TXT format]") | |
103 parser.add_option("-o", "--output", dest="outputFile", action="store", type="string", help="output file [format: output file in sequence format given by -f]") | |
104 parser.add_option("-x", "--exclude", dest="exclude", action="store_true", default=False, help="output all those whose name is NOT on the list [format: boolean]") | |
105 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") | |
106 (options, args) = parser.parse_args() | |
107 | |
108 rsl = RestrictSequenceList(options.verbosity) | |
109 rsl.setInputFileName(options.inputFile, options.format) | |
110 rsl.setOutputFileName(options.outputFile, options.format) | |
111 rsl.setNamesFileName(options.names) | |
112 rsl.setExclusion(options.exclude) | |
113 rsl.run() |