Mercurial > repos > yufei-luo > s_mart
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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| children |
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| -1:000000000000 | 0:e0f8dcca02ed |
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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 |