Mercurial > repos > yufei-luo > s_mart
changeset 48:809ed01c8014
Deleted selected files
| author | m-zytnicki |
|---|---|
| date | Mon, 09 Dec 2013 04:29:22 -0500 |
| parents | b6481845eb0d |
| children | 80a080dc3ee8 |
| files | SMART/Java/Python/compareOverlapping.py |
| diffstat | 1 files changed, 0 insertions(+), 126 deletions(-) [+] |
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--- a/SMART/Java/Python/compareOverlapping.py Mon Sep 30 05:51:28 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,126 +0,0 @@ -#! /usr/bin/env python -# -# Copyright INRA-URGI 2009-2010 -# -# This software is governed by the CeCILL license under French law and -# abiding by the rules of distribution of free software. You can use, -# modify and/ or redistribute the software under the terms of the CeCILL -# license as circulated by CEA, CNRS and INRIA at the following URL -# "http://www.cecill.info". -# -# As a counterpart to the access to the source code and rights to copy, -# modify and redistribute granted by the license, users are provided only -# with a limited warranty and the software's author, the holder of the -# economic rights, and the successive licensors have only limited -# liability. -# -# In this respect, the user's attention is drawn to the risks associated -# with loading, using, modifying and/or developing or reproducing the -# software by the user in light of its specific status of free software, -# that may mean that it is complicated to manipulate, and that also -# therefore means that it is reserved for developers and experienced -# professionals having in-depth computer knowledge. Users are therefore -# encouraged to load and test the software's suitability as regards their -# requirements in conditions enabling the security of their systems and/or -# data to be ensured and, more generally, to use and operate it in the -# same conditions as regards security. -# -# The fact that you are presently reading this means that you have had -# knowledge of the CeCILL license and that you accept its terms. -# -"""Compare overlap of two transcript lists""" -import sys -import os -from optparse import OptionParser -from SMART.Java.Python.misc import Utils -from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer -from commons.core.writer.TranscriptWriter import TranscriptWriter -from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator -from SMART.Java.Python.misc.RPlotter import RPlotter -from commons.core.writer.Gff3Writer import Gff3Writer - -class CompareOverlapping(object): - - def __init__(self): - self._options = None - - - def setAttributesFromCmdLine(self): - description = "Compare Overlapping v1.0.3: Get the data which overlap with a reference set. [Category: Data Comparison]" - - parser = OptionParser(description = description) - parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]") - parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of file 1 [compulsory] [format: transcript file format]") - parser.add_option("-j", "--input2", dest="inputFileName2", action="store", type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]") - parser.add_option("-g", "--format2", dest="format2", action="store", type="string", help="format of file 2 [compulsory] [format: transcript file format]") - parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]") - parser.add_option("-S", "--start1", dest="start1", action="store", default=None, type="int", help="only consider the n first nucleotides of the transcripts in file 1 (do not use it with -U) [format: int]") - parser.add_option("-s", "--start2", dest="start2", action="store", default=None, type="int", help="only consider the n first nucleotides of the transcripts in file 2 (do not use it with -u) [format: int]") - parser.add_option("-U", "--end1", dest="end1", action="store", default=None, type="int", help="only consider the n last nucleotides of the transcripts in file 1 (do not use it with -S) [format: int]") - parser.add_option("-u", "--end2", dest="end2", action="store", default=None, type="int", help="only consider the n last nucleotides of the transcripts in file 2 (do not use it with -s) [format: int]") - parser.add_option("-t", "--intron", dest="introns", action="store_true", default=False, help="also report introns [format: bool] [default: false]") - parser.add_option("-E", "--5primeExtension1", dest="fivePrime1", action="store", default=None, type="int", help="extension towards 5' in file 1 [format: int]") - parser.add_option("-e", "--5primeExtension2", dest="fivePrime2", action="store", default=None, type="int", help="extension towards 5' in file 2 [format: int]") - parser.add_option("-N", "--3primeExtension1", dest="threePrime1", action="store", default=None, type="int", help="extension towards 3' in file 1 [format: int]") - parser.add_option("-n", "--3primeExtension2", dest="threePrime2", action="store", default=None, type="int", help="extension towards 3' in file 2 [format: int]") - parser.add_option("-c", "--colinear", dest="colinear", action="store_true", default=False, help="colinear only [format: bool] [default: false]") - parser.add_option("-a", "--antisense", dest="antisense", action="store_true", default=False, help="antisense only [format: bool] [default: false]") - parser.add_option("-d", "--distance", dest="distance", action="store", default=None, type="int", help="accept some distance between query and reference [format: int]") - parser.add_option("-k", "--included", dest="included", action="store_true", default=False, help="keep only elements from file 1 which are included in an element of file 2 [format: bool] [default: false]") - parser.add_option("-K", "--including", dest="including", action="store_true", default=False, help="keep only elements from file 2 which are included in an element of file 1 [format: bool] [default: false]") - parser.add_option("-m", "--minOverlap", dest="minOverlap", action="store", default=1, type="int", help="minimum number of nucleotides overlapping to declare an overlap [format: int] [default: 1]") - parser.add_option("-p", "--pcOverlap", dest="pcOverlap", action="store", default=None, type="int", help="minimum percentage of nucleotides to overlap to declare an overlap [format: int]") - parser.add_option("-O", "--notOverlapping", dest="notOverlapping", action="store_true", default=False, help="also output not overlapping data [format: bool] [default: false]") - parser.add_option("-x", "--exclude", dest="exclude", action="store_true", default=False, help="invert the match [format: bool] [default: false]") - parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") - parser.add_option("-l", "--log", dest="log", action="store_true", default=False, help="write a log file [format: bool] [default: false]") - (self._options, args) = parser.parse_args() - - - def run(self): - logHandle = None - if self._options.log: - logHandle = open(self._options.output, "w") - - transcriptContainer1 = TranscriptContainer(self._options.inputFileName1, self._options.format1, self._options.verbosity) - transcriptContainer2 = TranscriptContainer(self._options.inputFileName2, self._options.format2, self._options.verbosity) - writer = TranscriptWriter(self._options.output, "gff3", self._options.verbosity) - - transcriptListComparator = TranscriptListsComparator(logHandle, self._options.verbosity) - transcriptListComparator.restrictToStart(transcriptListComparator.QUERY, self._options.start1) - transcriptListComparator.restrictToStart(transcriptListComparator.REFERENCE, self._options.start2) - transcriptListComparator.restrictToEnd(transcriptListComparator.QUERY, self._options.end1) - transcriptListComparator.restrictToEnd(transcriptListComparator.REFERENCE, self._options.end2) - transcriptListComparator.extendFivePrime(transcriptListComparator.QUERY, self._options.fivePrime1) - transcriptListComparator.extendFivePrime(transcriptListComparator.REFERENCE, self._options.fivePrime2) - transcriptListComparator.extendThreePrime(transcriptListComparator.QUERY, self._options.threePrime1) - transcriptListComparator.extendThreePrime(transcriptListComparator.REFERENCE, self._options.threePrime2) - transcriptListComparator.acceptIntrons(transcriptListComparator.QUERY, self._options.introns) - transcriptListComparator.acceptIntrons(transcriptListComparator.REFERENCE, self._options.introns) - transcriptListComparator.getAntisenseOnly(self._options.antisense) - transcriptListComparator.getColinearOnly(self._options.colinear) - transcriptListComparator.getInvert(self._options.exclude) - transcriptListComparator.setMaxDistance(self._options.distance) - transcriptListComparator.setMinOverlap(self._options.minOverlap) - transcriptListComparator.setPcOverlap(self._options.pcOverlap) - transcriptListComparator.setIncludedOnly(self._options.included) - transcriptListComparator.setIncludingOnly(self._options.including) - transcriptListComparator.includeNotOverlapping(self._options.notOverlapping) - transcriptListComparator.computeOdds(True) - transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer1) - transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.REFERENCE, transcriptContainer2) - transcriptListComparator.setOutputWriter(writer) - transcriptListComparator.compareTranscriptList() - - if self._options.log: - logHandle.close() - - if not self._options.exclude: - odds = transcriptListComparator.getOdds() - if self._options.verbosity > 0 and odds: - print "min/avg/med/max transcripts: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(odds) - -if __name__ == "__main__": - icompareOverlapping = CompareOverlapping() - icompareOverlapping.setAttributesFromCmdLine() - icompareOverlapping.run()