comparison smart_toolShed/SMART/Java/Python/WrappGetReadDistribution.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
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