Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/modifyGenomicCoordinates.py @ 38:2c0c0a89fad7
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| author | m-zytnicki |
|---|---|
| date | Thu, 02 May 2013 09:56:47 -0400 |
| parents | 769e306b7933 |
| children |
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| 37:d22fadc825e3 | 38:2c0c0a89fad7 |
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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 genomic coordinates of a file""" | |
| 32 | |
| 33 from optparse import OptionParser | |
| 34 from commons.core.writer.TranscriptWriter import TranscriptWriter | |
| 35 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer | |
| 36 from SMART.Java.Python.misc.Progress import Progress | |
| 37 | |
| 38 | |
| 39 if __name__ == "__main__": | |
| 40 | |
| 41 # parse command line | |
| 42 description = "Modify Genomic Coordinates v1.0.1: Extend or shrink a list of genomic coordinates. [Category: Data Modification]" | |
| 43 | |
| 44 parser = OptionParser(description = description) | |
| 45 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]") | |
| 46 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the input [compulsory] [format: transcript file format]") | |
| 47 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]") | |
| 48 parser.add_option("-s", "--start", dest="start", action="store", default=None, type="int", help="restrict to the start of the transcript [format: int]") | |
| 49 parser.add_option("-e", "--end", dest="end", action="store", default=None, type="int", help="restrict to the end of the transcript [format: int]") | |
| 50 parser.add_option("-5", "--fivePrime", dest="fivePrime", action="store", default=None, type="int", help="extend to the 5' direction [format: int]") | |
| 51 parser.add_option("-3", "--threePrime", dest="threePrime", action="store", default=None, type="int", help="extend to the 3' direction [format: int]") | |
| 52 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") | |
| 53 | |
| 54 (options, args) = parser.parse_args() | |
| 55 | |
| 56 parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity) | |
| 57 | |
| 58 writer = TranscriptWriter(options.outputFileName, "gff3", options.verbosity) | |
| 59 | |
| 60 nbItems = 0 | |
| 61 nbItems = parser.getNbItems() | |
| 62 print "%i items found" % (nbItems) | |
| 63 | |
| 64 progress = Progress(nbItems, "Analyzing sequences of " + options.inputFileName, options.verbosity) | |
| 65 for transcript in parser.getIterator(): | |
| 66 if options.start != None: | |
| 67 transcript.restrictStart(options.start) | |
| 68 if options.end != None: | |
| 69 transcript.restrictEnd(options.end) | |
| 70 if options.fivePrime != None: | |
| 71 transcript.extendStart(options.fivePrime) | |
| 72 if options.threePrime != None: | |
| 73 transcript.extendEnd(options.threePrime) | |
| 74 | |
| 75 writer.addTranscript(transcript) | |
| 76 | |
| 77 progress.inc() | |
| 78 progress.done() | |
| 79 | |
| 80 writer.write() |