cistematic/experiments/phyloFoot.py

   1 ###########################################################################
   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                                 #
   6 #                                                                         #
   7 #    All Rights Reserved.                                                 #
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  14 # and to permit persons to whom the Software is furnished to do so,       #
  15 # subject to the following conditions:                                    #
  16 #                                                                         #
  17 # The above copyright notice and this permission notice shall be          #
  18 # included in all copies or substantial portions of the Software.         #
  19 #                                                                         #
  20 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,         #
  21 # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF      #
  22 # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                   #
  23 # NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS     #
  24 # BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN      #
  25 # ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN       #
  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 from conservation import Conservation
  34 from draw import Draw
  35 from cistematic.core.homology import homologyDB
  36
  37 class PhyloFoot(Experiment, AnalyzeMotifs, Conservation, Draw):
  38     experimentType = "phyloFoot"
  39     startingGenome = "scerevisiae"
  40     targetGenomes = []
  41     refGenes = []
  42     phyloMap = {}
  43     useConservation = True
  44
  45
  46     def initialize(self, sGenome="", rGenes=[], tGenomes=[], analysisDB="", conservationDB="", maskNonConserved=True):
  47         wholeDataset = []
  48         try:
  49             self.createAnalysis(dbName=analysisDB)
  50             if self.consDBName == "":
  51                 self.createConservation(dbName=conservationDB)
  52         except:
  53             pass
  54
  55         if sGenome == "":
  56             sGenome = self.startingGenome
  57         else:
  58             self.startingGenome = sGenome
  59
  60         if len(rGenes) == 0:
  61             rGenes = self.refGenes
  62         else:
  63             self.refGenes = rGenes
  64
  65         if len(tGenomes) == 0:
  66             tGenomes = self.targetGenomes
  67         else:
  68             self.targetGenomes = tGenomes
  69
  70         self.useConservation = maskNonConserved
  71         try:
  72             for gene in rGenes:
  73                 wholeDataset.append((sGenome, [gene]))
  74                 hGenes = self.returnHomologs((sGenome, gene))
  75                 self.phyloMap[(sGenome, gene)] = hGenes
  76                 for oneGene in hGenes:
  77                     wholeDataset.append((oneGene[0], [oneGene[1]]))
  78         except:
  79             self.mlog("could not load from homology for (%s,%s,%s)" % (sGenome, str(rGenes), str(tGenomes)))
  80
  81         Experiment.initialize(self, wholeDataset)
  82
  83
  84     def run(self):
  85         for gene in self.refGenes:
  86             dset = self.phyloMap[(self.startingGenome, gene)]
  87             dset.append((self.startingGenome, gene))
  88             datasetID = self.setSettingsID("dataset-%s-%s" % (self.startingGenome, gene), dset)
  89             if self.useConservation:
  90                 fastaFile = self.createDataFile(datasetID, geneDict= self.maskNonConservedSequence(datasetID))
  91             else:
  92                 fastaFile = self.createDataFile(datasetID)
  93
  94             for (prog, settingsID) in self.programs:
  95                 prog.inputFile(fastaFile)
  96                 runID = self.setRun(prog.name(), datasetID, settingsID)
  97                 tag = str(runID)
  98                 prog.setTagID(tag)
  99                 if True:
 100                     prog.run()
 101                     theMotifs = prog.getMotifs()
 102                     for mot in theMotifs:
 103                         self.appendResults(mot)
 104                 else:
 105                     self.mlog("problem with run %s" % tag)