cistematic/experiments/varyLength.py

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   2 #                                                                         #
   3 # C O P Y R I G H T   N O T I C E                                         #
   4 #  Copyright (c) 2003-10 by:                                              #
   5 #    * California Institute of Technology                                 #
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  20 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,         #
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  22 # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                   #
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  26 # CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE        #
  27 # SOFTWARE.                                                               #
  28 ###########################################################################
  29 #
  30 # a simple use of the experiment class
  31 from experiment import Experiment
  32 from analyzeMotifs import AnalyzeMotifs
  33
  34 class VaryLength(Experiment, AnalyzeMotifs):
  35     experimentType = "varyLength"
  36
  37
  38     def setRange(self, step, uMin=0, uMax=0, dMin=0, dMax=0):
  39         self.stepSize      = step
  40         self.upstreamMin   = uMin
  41         self.upstreamMax   = uMax + 1
  42         self.downstreamMin = dMin
  43         self.downstreamMax = dMax + 1
  44
  45
  46     def run(self):
  47         Experiment.run(self)
  48
  49         for downP in range(self.downstreamMin, self.downstreamMax, self.stepSize):
  50             for upP in range(self.upstreamMin, self.upstreamMax, self.stepSize):
  51                 self.setSeqParameters(upP, downP)
  52                 # force reloading of the genepool
  53                 self.loadGenepool()
  54                 datasetID = self.genepoolID
  55                 fastaFile = self.createDataFile()
  56                 for (prog, settingsID) in self.programs:
  57                     prog.inputFile(fastaFile)
  58                     # reset setttings to orig settings, set new length, save settings
  59                     prog.setSettings(self.settings[settingsID])
  60                     prog.setSeqLength(str(upP + downP))
  61                     newestSettingsID = self.setSettings(prog.getSettings())
  62                     runID = self.setRun(prog.name(), datasetID, newestSettingsID)
  63                     tag = str(runID)
  64                     prog.setTagID(tag)
  65                     prog.run()
  66                     theMotifs = prog.getMotifs()
  67                     for mot in theMotifs:
  68                         self.results.append(mot)