6
+ − 1 #! /usr/bin/env python
+ − 2 from optparse import OptionParser
+ − 3 import tarfile
+ − 4 import os
+ − 5 import re
+ − 6 import shutil
+ − 7 import subprocess
+ − 8
+ − 9 SMART_PATH = "%sSMART" % os.environ["REPET_PATH"]
+ − 10
+ − 11 def toTar(tarFileName, directory):
+ − 12 fileName = os.path.splitext(tarFileName)[0]
+ − 13 fileNameBaseName = os.path.basename(fileName)
+ − 14 tfile = tarfile.open(fileName + ".tmp.tar", "w")
+ − 15 list = os.listdir(directory)
+ − 16 for file in list:
+ − 17 if re.search(str(fileNameBaseName), file):
+ − 18 tfile.add(file)
+ − 19 os.system("mv %s %s" % (fileName + ".tmp.tar", options.outTarFileName))
+ − 20 tfile.close()
+ − 21
+ − 22
+ − 23 if __name__ == "__main__":
+ − 24
+ − 25 magnifyingFactor = 1000
+ − 26
+ − 27 # parse command line
+ − 28 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]"
+ − 29
+ − 30
+ − 31 parser = OptionParser(description = description)
+ − 32 parser.add_option("-i", "--input",dest="inputFileName",action="store",type="string",help="input file name [compulsory] [format: file in GFF3 format]")
+ − 33 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]")
+ − 34 parser.add_option("-o", "--output",dest="outTarFileName",action="store",type="string", help="output file [compulsory] [format: output file tar format]")
+ − 35 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]")
+ − 36 parser.add_option("-f", "--format",dest="format",action="store",default="png",type="string", help="format of the output file [format: string] [default: png]")
+ − 37 parser.add_option("-r", "--normalize",dest="normalize",action="store_true", default=False,help="normalize data (when panels are different) [format: bool] [default: false]")
+ − 38 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]")
+ − 39 parser.add_option("-v", "--verbosity",dest="verbosity",action="store",default=1,type="int",help="trace level [format: int]")
+ − 40 (options, args) = parser.parse_args()
+ − 41
+ − 42
+ − 43 absPath = os.getcwd()
+ − 44 print "the current path is :", absPath
+ − 45 directory = "/tmp/wrappPlotRepartition"
+ − 46 print "the dir path is :", directory
+ − 47 if not os.path.exists(directory):
+ − 48 os.makedirs(directory)
+ − 49 os.chdir(directory)
+ − 50 if options.inputFileName != None and options.format != None and options.outTarFileName != None:
+ − 51 outputFileName = os.path.splitext(os.path.basename(options.outTarFileName))[0]
+ − 52 cmd = "python %s/Java/Python/plotRepartition.py -i %s -o %s -D %s" % (SMART_PATH, options.inputFileName, outputFileName, directory)
+ − 53 if options.names != None :
+ − 54 cmd += " -n %s" % options.names
+ − 55 else: print "You must choose tag names !"
+ − 56 if options.colors != None :
+ − 57 cmd += " -c %s" % options.colors
+ − 58 if options.format != None:
+ − 59 cmd += " -f %s" % options.format
+ − 60 if options.normalize :
+ − 61 cmd += " -r "
+ − 62 if options.log != "" :
+ − 63 cmd += " -l %s" % options.log
+ − 64
+ − 65 print "cmd is: ", cmd
+ − 66 status = subprocess.call(cmd, shell=True)
+ − 67 if status != 0:
+ − 68 raise Exception("Problem with the execution of command!")
+ − 69 toTar(options.outTarFileName, directory)
+ − 70 shutil.rmtree(directory)
+ − 71
