Mercurial > repos > yufei-luo > s_mart

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

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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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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #! /usr/bin/env python
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 from optparse import OptionParser
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 import tarfile
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 import os
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 import re
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 import shutil
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 import subprocess
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9 SMART_PATH = "%s/SMART" % os.environ["REPET_PATH"]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 def toTar(tarFileName, directory):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 fileName = os.path.splitext(tarFileName)[0]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 fileNameBaseName = os.path.basename(fileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 tfile = tarfile.open(fileName + ".tmp.tar", "w")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 list = os.listdir(directory)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 for file in list:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 if re.search(str(fileNameBaseName), file):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 tfile.add(file)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 os.system("mv %s %s" % (fileName + ".tmp.tar", options.outTarFileName))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 tfile.close()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 if __name__ == "__main__":
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # parse command line
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 description = "Get Read Distribution v1.0.1: Plot the number of identical reads and give the most represented. [Category: Visualization]"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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27
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28 parser = OptionParser(description = description)
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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]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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30 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of the file [compulsory] [format: sequence file format]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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31 parser.add_option("-n", "--number", dest="number", action="store", default=None, type="int", help="keep the best n [format: int]")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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32 parser.add_option("-p", "--percent", dest="percent", action="store", default=None, type="float", help="keep the best n\% [format: float]")
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33 parser.add_option("-o", "--output", dest="outTarFileName", action="store", type="string", help="output file [compulsory] [format: zip]")
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35 (options, args) = parser.parse_args()
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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38 absPath = os.getcwd()
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39 print "the current path is :", absPath
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40 directory = "/tmp/wrappGetReadDistribution"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41 print "the dir path is :", directory
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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42 if not os.path.exists(directory):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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43 os.makedirs(directory)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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44 os.chdir(directory)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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45 if options.inputFileName != None and options.format != None and options.outTarFileName != None:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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46 outputFileName = os.path.splitext(os.path.basename(options.outTarFileName))[0]
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 cmd = "python %s/Java/Python/getReadDistribution.py -i %s -f %s -o %s -D %s" % (SMART_PATH, options.inputFileName, options.format, outputFileName, directory)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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48 if options.number != None :
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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49 cmd += " -n %s" % options.number
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50 if options.percent != None :
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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51 cmd += " -p %s" % options.percent
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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52 print "cmd is: ", cmd
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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53 status = subprocess.call(cmd, shell=True)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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54 if status != 0:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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55 raise Exception("Problem with the execution of command!")
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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56 toTar(options.outTarFileName, directory)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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57 shutil.rmtree(directory)
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58