Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/restrictFromNucleotides.py @ 6:769e306b7933
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| author | yufei-luo |
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| date | Fri, 18 Jan 2013 04:54:14 -0500 |
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| 5:ea3082881bf8 | 6:769e306b7933 |
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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 """Remove all dirty sequences""" | |
| 32 | |
| 33 import os | |
| 34 import sys | |
| 35 from optparse import OptionParser | |
| 36 from commons.core.parsing.FastaParser import * | |
| 37 from commons.core.writer.FastaWriter import * | |
| 38 from commons.core.parsing.FastqParser import * | |
| 39 from commons.core.writer.FastqWriter import * | |
| 40 from SMART.Java.Python.misc.Progress import * | |
| 41 from SMART.Java.Python.misc.RPlotter import * | |
| 42 | |
| 43 | |
| 44 if __name__ == "__main__": | |
| 45 | |
| 46 # parse command line | |
| 47 description = "Restrict from nucleotide v1.0.1: Remove the sequences with ambiguous nucleotides. [Category: Personal]" | |
| 48 | |
| 49 parser = OptionParser(description = description) | |
| 50 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in sequence format given by -f]") | |
| 51 parser.add_option("-f", "--format", dest="inputFileName", action="store", default="fasta", type="string", help="format of the input and output files [compulsory] [format: sequence file format]") | |
| 52 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in sequence format given by -f]") | |
| 53 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") | |
| 54 parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]") | |
| 55 (options, args) = parser.parse_args() | |
| 56 | |
| 57 # treat items | |
| 58 if options.format == "fasta": | |
| 59 parser = FastaParser(options.inputFileName, options.verbosity) | |
| 60 writer = FastaWriter(options.outputFileName, options.verbosity) | |
| 61 elif options.format == "fastq": | |
| 62 parser = FastqParser(options.inputFileName, options.verbosity) | |
| 63 writer = FastqWriter(options.outputFileName, options.verbosity) | |
| 64 else: | |
| 65 sys.exit("Do not understand '%s' format." % (options.format)) | |
| 66 nbSequences = parser.getNbSequences() | |
| 67 print "sequences: %d" % (nbSequences) | |
| 68 | |
| 69 progress = Progress(nbSequences, "Analyzing sequences of %s" % (options.inputFileName), options.verbosity) | |
| 70 nbKept = 0 | |
| 71 for sequence in parser.getIterator(): | |
| 72 if not sequence.containsAmbiguousNucleotides(): | |
| 73 writer.addSequence(sequence) | |
| 74 nbKept += 1 | |
| 75 progress.inc() | |
| 76 progress.done() | |
| 77 | |
| 78 print "%d items, %d kept (%.2f%%)" % (nbSequences, nbKept, float(nbKept) / nbSequences * 100) |