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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 """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)