annotate SMART/Java/Python/WrappGetReadDistribution.py @ 53:47310c4fb725

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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 = "%s/SMART" % 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     # parse command line
26     description = "Get Read Distribution v1.0.1: Plot the number of identical reads and give the most represented. [Category: Visualization]"
27 
28     parser = OptionParser(description = description)
29     parser.add_option("-i", "--input",     dest="inputFileName",  action="store",               type="string", help="input file sequence [compulsory] [format: file in sequence format given by -f]")
30     parser.add_option("-f", "--format",    dest="format",         action="store",               type="string", help="format of the file [compulsory] [format: sequence file format]")
31     parser.add_option("-n", "--number",    dest="number",         action="store", default=None, type="int",    help="keep the best n    [format: int]")
32     parser.add_option("-p", "--percent",   dest="percent",        action="store", default=None, type="float",  help="keep the best n\% [format: float]")
33     parser.add_option("-o", "--output",    dest="outTarFileName", action="store",               type="string", help="output file [compulsory] [format: zip]")
34 
35     (options, args) = parser.parse_args()
36 
37 
38     absPath = os.getcwd()
39     print "the current path is :", absPath
40     directory = "/tmp/wrappGetReadDistribution"
41     print "the dir path is :", directory
42     if not os.path.exists(directory):
43         os.makedirs(directory)
44     os.chdir(directory)
45     if options.inputFileName != None and options.format != None and options.outTarFileName != None:
46         outputFileName = os.path.splitext(os.path.basename(options.outTarFileName))[0]
47         cmd = "python %s/Java/Python/getReadDistribution.py -i %s -f %s -o %s -D %s" % (SMART_PATH, options.inputFileName, options.format, outputFileName, directory)
48     if options.number != None :
49         cmd += " -n %s" % options.number
50     if options.percent != None :
51         cmd += " -p %s" % options.percent
52     print "cmd is: ", cmd    
53     status = subprocess.call(cmd, shell=True)
54     if status != 0:
55             raise Exception("Problem with the execution of command!")
56     toTar(options.outTarFileName, directory)
57     shutil.rmtree(directory)
58