Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/runRandomJobs.py @ 71:d96f6c9a39e0 draft default tip
Removed pyc files.
author | m-zytnicki |
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date | Thu, 07 Apr 2016 09:25:18 -0400 |
parents | 769e306b7933 |
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import unittest import os import time from optparse import OptionParser from SMART.Java.Python.ncList.test.MockFindOverlaps_randomExample import MockFindOverlaps_randomExample from SMART.Java.Python.FindOverlapsOptim import FindOverlapsOptim if __name__ == '__main__': description = "runRandomJobs: create random ref/query files (with size given), and run the jobs on cluster with help of runJobs.sh" parser = OptionParser(description = description) parser.add_option("-i", "--inputRef", dest="inputRefGff3FileName", action="store", type="string", help="Reference input file [compulsory] [format: file in gff3 format]") parser.add_option("-j", "--inputQuery", dest="inputQueryGff3FileName", action="store", type="string", help="Query input file [compulsory] [format: file in gff3 format]") parser.add_option("-m", "--inputRefSize", dest="numberOfRefReads", action="store", type="int", help="The number of Reference") parser.add_option("-n", "--inputQuerySize", dest="numberOfQReads", action="store", type="int", help="The number of Query") parser.add_option("-o", "--output", dest="outputGff3FileName", action="store", type="string", help="output file [compulsory] [format: output file in gff3 format]") (options, args) = parser.parse_args() outputDataName = 'timeResult.dat' fTime = open(outputDataName, 'w') fTime.write('NbRef\tNbQuery\tNbOverlap\ttime\n') chromSize = 100000 print 'ref size = %d, query size = %d' %(options.numberOfRefReads, options.numberOfQReads) iMFOR_ref = MockFindOverlaps_randomExample(options.inputRefGff3FileName, 'ref', options.numberOfRefReads, chromSize) iMFOR_ref.write() cmd_ref = 'sort -f -n -k4 -k5.4rn -o %s %s' % (options.inputRefGff3FileName, options.inputRefGff3FileName) os.system(cmd_ref) iMFOR_query = MockFindOverlaps_randomExample(options.inputQueryGff3FileName,'q', options.numberOfQReads, chromSize) iMFOR_query.write() cmd_query = 'sort -f -n -k4 -k5.4rn -o %s %s' % (options.inputQueryGff3FileName, options.inputQueryGff3FileName) os.system(cmd_query) iFOO = FindOverlaps_optim(options.inputRefGff3FileName, options.inputQueryGff3FileName) iFOO.setOutputGff3FileName(options.outputGff3FileName) startTime_optim = time.time() iFOO.run() iFOO.close() nbOverlap = iFOO.getNbOverlap() endTime_optim = time.time() cmd = 'sort -f -n -k4 -k5.4rn -k9.5 -t ";" -o %s %s' % (options.outputGff3FileName, options.outputGff3FileName) os.system(cmd) totalTime_optim = endTime_optim - startTime_optim print 'we take %s second.' % (totalTime_optim) fTime.write('%d\t%d\t%d\t%.2f\n'%(options.numberOfRefReads, options.numberOfQReads, nbOverlap, totalTime_optim)) iFOO.deletIntermediateFiles() fTime.close()