cistematic/experiments/locate.py

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   4 #  Copyright (c) 2003-10 by:                                              #
   5 #    * California Institute of Technology                                 #
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  27 # SOFTWARE.                                                               #
  28 ###########################################################################
  29 #
  30 # The locate class allows mapping of known motifs to sequences or genomes
  31 # should only be used with the Locator program, for now
  32 from experiment import Experiment
  33 from analyzeMotifs import AnalyzeMotifs
  34 from cistematic.core import getChromosomeNames, readChromosome
  35
  36 class Locate(Experiment, AnalyzeMotifs):
  37     experimentType = "locate"
  38
  39
  40     def getChromosomeList(self, genome, partition=1, slice=0, db=""):
  41         """ return a list of the chromosomes available for a given genome.
  42         """
  43         result = []
  44         try:
  45             chromList = getChromosomeNames(genome, db, partition, slice)
  46         except:
  47             chromList = []
  48
  49         for entry in chromList:
  50             result.append((genome, entry))
  51
  52         return result
  53
  54
  55     def initialize(self, listType, compoundList):
  56         """ must initialize with listType='chromosome' in order to scan chromosomes
  57         """
  58         self.genepool = {}
  59         genepoolKeys = []
  60         if listType == "chromosome":
  61             for (genome, chromName) in compoundList:
  62                 self.genepool[(genome, chromName)] = readChromosome(genome, chromName)
  63                 genepoolKeys.append("%s\t%s" % (genome, chromName))
  64
  65             self.genepoolID = self.setSettings("chromolist", genepoolKeys)
  66         else:
  67             Experiment.initialize(self, compoundList)
  68
  69
  70     def run(self):
  71         Experiment.run(self)
  72         datasetID = self.genepoolID
  73         for (prog, settingsID) in self.programs:
  74             try:
  75                 if prog.name() == "Locator":
  76                     (settingName, settingData) = self.getSettingsID(settingsID)
  77                     prog.setSettings(settingData)
  78                     runID = self.setRun(prog.name(), datasetID, settingsID)
  79                     tag = str(runID)
  80                     prog.setTagID(tag)
  81                     prog.run()
  82                     theMotifs = prog.getMotifs()
  83                     for mot in theMotifs:
  84                         self.appendResults(mot)
  85                 else:
  86                     self.mlog("Can only run Locate experiment with Locator program")
  87             except:
  88                 self.mlog("Error running program %s with settings %s" % (prog, settingsID))