comparison SMART/Java/Python/restrictFromSize.py @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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35:d94018ca4ada 36:44d5973c188c
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 """Get the size distribution of a Fasta / BED file"""
32
33 import os
34 from optparse import OptionParser
35 from commons.core.parsing.FastaParser import *
36 from commons.core.parsing.FastqParser import *
37 from SMART.Java.Python.structure.TranscriptContainer import *
38 from commons.core.writer.TranscriptWriter import *
39 from commons.core.writer.FastaWriter import *
40 from commons.core.writer.FastqWriter import *
41 from SMART.Java.Python.misc.Progress import *
42 from SMART.Java.Python.misc.RPlotter import *
43
44
45 if __name__ == "__main__":
46
47 # parse command line
48 description = "Restrict from Size v1.0.1: Select the elements of a list of sequences or transcripts with a given size. [Category: Data Selection]"
49
50 parser = OptionParser(description = description)
51 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript or sequence format given by -f]")
52 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input [compulsory] [format: sequence or transcript file format]")
53 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in transcript or sequence format given by -f]")
54 parser.add_option("-m", "--minSize", dest="minSize", action="store", default=None, type="int", help="minimum size [format: int]")
55 parser.add_option("-M", "--maxSize", dest="maxSize", action="store", default=None, type="int", help="maximum size [format: int]")
56 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
57 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]")
58 (options, args) = parser.parse_args()
59
60 if options.format == "fasta":
61 parser = FastaParser(options.inputFileName, options.verbosity)
62 writer = FastaWriter(options.outputFileName, options.verbosity)
63 elif options.format == "fastq":
64 parser = FastqParser(options.inputFileName, options.verbosity)
65 writer = FastqWriter(options.outputFileName, options.verbosity)
66 else:
67 parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
68 writer = TranscriptWriter(options.outputFileName, options.format, options.verbosity)
69
70
71 # treat items
72 nbItems = parser.getNbItems()
73 progress = Progress(nbItems, "Analyzing sequences of %s" % (options.inputFileName), options.verbosity)
74 nbKept = 0
75 nbRead = 0
76 nbClKept = 0
77 nbClRead = 0
78 for item in parser.getIterator():
79 size = item.getSize()
80 nb = 1 if options.format in ("fasta", "fastq") or "nbElements" not in item.getTagNames() else float(item.getTagValue("nbElements"))
81 nbRead += nb
82 nbClRead += 1
83 if (options.minSize == None or options.minSize <= size) and (options.maxSize == None or options.maxSize >= size):
84 writer.addElement(item)
85 nbKept += nb
86 nbClKept += 1
87 progress.inc()
88 progress.done()
89
90 writer.write()
91
92 print "%d items, %d kept (%.2f%%)" % (nbRead, nbKept, 0 if nbItems == 0 else float(nbKept) / nbItems * 100)
93 if nbKept != nbClKept or nbRead != nbClRead:
94 print "%d clusters, %d kept (%.2f%%)" % (nbClRead, nbClKept, 0 if nbClRead == 0 else float(nbClKept) / nbClRead * 100)