Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/WrappPlotRepartition.py @ 9:1eb55963fe39
Updated CompareOverlappingSmall*.py
author | m-zytnicki |
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date | Thu, 14 Mar 2013 05:23:05 -0400 |
parents | 769e306b7933 |
children |
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#! /usr/bin/env python from optparse import OptionParser import tarfile import os import re import shutil import subprocess SMART_PATH = "%sSMART" % os.environ["REPET_PATH"] def toTar(tarFileName, directory): fileName = os.path.splitext(tarFileName)[0] fileNameBaseName = os.path.basename(fileName) tfile = tarfile.open(fileName + ".tmp.tar", "w") list = os.listdir(directory) for file in list: if re.search(str(fileNameBaseName), file): tfile.add(file) os.system("mv %s %s" % (fileName + ".tmp.tar", options.outTarFileName)) tfile.close() if __name__ == "__main__": magnifyingFactor = 1000 # parse command line description = "Plot the repartition of different data on a whole genome. (This tool uses 1 input file only, the different values being stored in the tags. See documentation to know more about it.) [Category: Visualization]" parser = OptionParser(description = description) parser.add_option("-i", "--input",dest="inputFileName",action="store",type="string",help="input file name [compulsory] [format: file in GFF3 format]") parser.add_option("-n", "--names",dest="names", action="store", type="string", help="name for the tags (separated by commas and no space) [compulsory] [format: string]") parser.add_option("-o", "--output",dest="outTarFileName",action="store",type="string", help="output file [compulsory] [format: output file tar format]") parser.add_option("-c", "--color",dest="colors",action="store",default=None,type="string", help="color of the lines (separated by commas and no space) [format: string]") parser.add_option("-f", "--format",dest="format",action="store",default="png",type="string", help="format of the output file [format: string] [default: png]") parser.add_option("-r", "--normalize",dest="normalize",action="store_true", default=False,help="normalize data (when panels are different) [format: bool] [default: false]") parser.add_option("-l", "--log",dest="log",action="store",default="",type="string", help="use log on x- or y-axis (write 'x', 'y' or 'xy') [format: string]") parser.add_option("-v", "--verbosity",dest="verbosity",action="store",default=1,type="int",help="trace level [format: int]") (options, args) = parser.parse_args() absPath = os.getcwd() print "the current path is :", absPath directory = "/tmp/wrappPlotRepartition" print "the dir path is :", directory if not os.path.exists(directory): os.makedirs(directory) os.chdir(directory) if options.inputFileName != None and options.format != None and options.outTarFileName != None: outputFileName = os.path.splitext(os.path.basename(options.outTarFileName))[0] cmd = "python %s/Java/Python/plotRepartition.py -i %s -o %s -D %s" % (SMART_PATH, options.inputFileName, outputFileName, directory) if options.names != None : cmd += " -n %s" % options.names else: print "You must choose tag names !" if options.colors != None : cmd += " -c %s" % options.colors if options.format != None: cmd += " -f %s" % options.format if options.normalize : cmd += " -r " if options.log != "" : cmd += " -l %s" % options.log print "cmd is: ", cmd status = subprocess.call(cmd, shell=True) if status != 0: raise Exception("Problem with the execution of command!") toTar(options.outTarFileName, directory) shutil.rmtree(directory)