Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/runRandomJobs.py @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
parents 769e306b7933
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37:d22fadc825e3 38:2c0c0a89fad7
1 import unittest
2 import os
3 import time
4 from optparse import OptionParser
5 from SMART.Java.Python.ncList.test.MockFindOverlaps_randomExample import MockFindOverlaps_randomExample
6 from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim
7
8 if __name__ == '__main__':
9 description = "runRandomJobs: create random ref/query files (with size given), and run the jobs on cluster with help of runJobs.sh"
10
11 parser = OptionParser(description = description)
12 parser.add_option("-i", "--inputRef", dest="inputRefGff3FileName", action="store", type="string", help="Reference input file [compulsory] [format: file in gff3 format]")
13 parser.add_option("-j", "--inputQuery", dest="inputQueryGff3FileName", action="store", type="string", help="Query input file [compulsory] [format: file in gff3 format]")
14 parser.add_option("-m", "--inputRefSize", dest="numberOfRefReads", action="store", type="int", help="The number of Reference")
15 parser.add_option("-n", "--inputQuerySize", dest="numberOfQReads", action="store", type="int", help="The number of Query")
16 parser.add_option("-o", "--output", dest="outputGff3FileName", action="store", type="string", help="output file [compulsory] [format: output file in gff3 format]")
17 (options, args) = parser.parse_args()
18
19 outputDataName = 'timeResult.dat'
20 fTime = open(outputDataName, 'w')
21 fTime.write('NbRef\tNbQuery\tNbOverlap\ttime\n')
22 chromSize = 100000
23 print 'ref size = %d, query size = %d' %(options.numberOfRefReads, options.numberOfQReads)
24 iMFOR_ref = MockFindOverlaps_randomExample(options.inputRefGff3FileName, 'ref', options.numberOfRefReads, chromSize)
25 iMFOR_ref.write()
26 cmd_ref = 'sort -f -n -k4 -k5.4rn -o %s %s' % (options.inputRefGff3FileName, options.inputRefGff3FileName)
27 os.system(cmd_ref)
28 iMFOR_query = MockFindOverlaps_randomExample(options.inputQueryGff3FileName,'q', options.numberOfQReads, chromSize)
29 iMFOR_query.write()
30 cmd_query = 'sort -f -n -k4 -k5.4rn -o %s %s' % (options.inputQueryGff3FileName, options.inputQueryGff3FileName)
31 os.system(cmd_query)
32 iFOO = FindOverlaps_optim(options.inputRefGff3FileName, options.inputQueryGff3FileName)
33 iFOO.setOutputGff3FileName(options.outputGff3FileName)
34
35 startTime_optim = time.time()
36 iFOO.run()
37 iFOO.close()
38 nbOverlap = iFOO.getNbOverlap()
39 endTime_optim = time.time()
40 cmd = 'sort -f -n -k4 -k5.4rn -k9.5 -t ";" -o %s %s' % (options.outputGff3FileName, options.outputGff3FileName)
41 os.system(cmd)
42 totalTime_optim = endTime_optim - startTime_optim
43 print 'we take %s second.' % (totalTime_optim)
44 fTime.write('%d\t%d\t%d\t%.2f\n'%(options.numberOfRefReads, options.numberOfQReads, nbOverlap, totalTime_optim))
45 iFOO.deletIntermediateFiles()
46 fTime.close()