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comparison SMART/Java/Python/restrictSequenceList.py @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
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()