Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/modifySequenceList.py @ 6:769e306b7933
Change the repository level.
| 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 """Modify the content of a FASTA file""" | |
| 32 import sys | |
| 33 from optparse import OptionParser | |
| 34 from commons.core.parsing.FastaParser import FastaParser | |
| 35 from commons.core.parsing.FastqParser import FastqParser | |
| 36 from commons.core.writer.FastaWriter import FastaWriter | |
| 37 from commons.core.writer.FastqWriter import FastqWriter | |
| 38 from SMART.Java.Python.misc.Progress import Progress | |
| 39 | |
| 40 | |
| 41 if __name__ == "__main__": | |
| 42 | |
| 43 # parse command line | |
| 44 description = "Modify Sequence List v1.0.1: Extend or shring a list of sequences. [Category: Data Modification]" | |
| 45 | |
| 46 parser = OptionParser(description = description) | |
| 47 parser.add_option("-i", "--input", dest="inputFileName",action="store", type="string", help="input file [compulsory] [format: file in format given by -f]") | |
| 48 parser.add_option("-o", "--output", dest="outputFileName", action="store",default=None, type="string", help="output file [compulsory] [format: output file in format given by -f]") | |
| 49 parser.add_option("-f", "--format", dest="format",action="store",type="string", help="format of the file [compulsory] [format: sequence file format]") | |
| 50 parser.add_option("-s", "--start", dest="start", action="store", default=None,type="int",help="keep first nucleotides [format: int]") | |
| 51 parser.add_option("-e", "--end", dest="end", action="store",default=None,type="int",help="keep last nucleotides [format: int]") | |
| 52 parser.add_option("-v", "--verbosity",dest="verbosity",action="store",default=1,type="int",help="trace level [format: int]") | |
| 53 (options, args) = parser.parse_args() | |
| 54 | |
| 55 if options.format == "fasta": | |
| 56 parser = FastaParser(options.inputFileName, options.verbosity) | |
| 57 writer = FastaWriter(options.outputFileName, options.verbosity) | |
| 58 elif options.format == "fastq": | |
| 59 parser = FastqParser(options.inputFileName, options.verbosity) | |
| 60 writer = FastqWriter(options.outputFileName, options.verbosity) | |
| 61 else: | |
| 62 sys.exit("Do not understand '%s' file format." % (options.format)) | |
| 63 | |
| 64 progress = Progress(parser.getNbSequences(), "Reading file %s" % (options.inputFileName), options.verbosity) | |
| 65 for sequence in parser.getIterator(): | |
| 66 if options.start != None: | |
| 67 sequence.shrinkToFirstNucleotides(options.start) | |
| 68 if options.end != None: | |
| 69 sequence.shrinkToLastNucleotides(options.end) | |
| 70 writer.addSequence(sequence) | |
| 71 progress.inc() | |
| 72 progress.done() |