erange 4.0a dev release with integrated cistematic

[erange.git] / cistematic / experiments / locate.py

diff --git a/cistematic/experiments/locate.py b/cistematic/experiments/locate.py
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+###########################################################################
+#                                                                         #
+# C O P Y R I G H T   N O T I C E                                         #
+#  Copyright (c) 2003-10 by:                                              #
+#    * California Institute of Technology                                 #
+#                                                                         #
+#    All Rights Reserved.                                                 #
+#                                                                         #
+# Permission is hereby granted, free of charge, to any person             #
+# obtaining a copy of this software and associated documentation files    #
+# (the "Software"), to deal in the Software without restriction,          #
+# including without limitation the rights to use, copy, modify, merge,    #
+# publish, distribute, sublicense, and/or sell copies of the Software,    #
+# and to permit persons to whom the Software is furnished to do so,       #
+# subject to the following conditions:                                    #
+#                                                                         #
+# The above copyright notice and this permission notice shall be          #
+# included in all copies or substantial portions of the Software.         #
+#                                                                         #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,         #
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF      #
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                   #
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS     #
+# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN      #
+# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN       #
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE        #
+# SOFTWARE.                                                               #
+###########################################################################
+#
+# The locate class allows mapping of known motifs to sequences or genomes
+# should only be used with the Locator program, for now
+from experiment import Experiment
+from analyzeMotifs import AnalyzeMotifs
+from cistematic.core import getChromosomeNames, readChromosome
+
+class Locate(Experiment, AnalyzeMotifs):
+    experimentType = "locate"
+
+
+    def getChromosomeList(self, genome, partition=1, slice=0, db=""):
+        """ return a list of the chromosomes available for a given genome.
+        """
+        result = []
+        try:
+            chromList = getChromosomeNames(genome, db, partition, slice)
+        except:
+            chromList = []
+
+        for entry in chromList:
+            result.append((genome, entry))
+
+        return result
+
+
+    def initialize(self, listType, compoundList):
+        """ must initialize with listType='chromosome' in order to scan chromosomes
+        """
+        self.genepool = {}
+        genepoolKeys = []
+        if listType == "chromosome":
+            for (genome, chromName) in compoundList:
+                self.genepool[(genome, chromName)] = readChromosome(genome, chromName)
+                genepoolKeys.append("%s\t%s" % (genome, chromName))
+
+            self.genepoolID = self.setSettings("chromolist", genepoolKeys)
+        else:
+            Experiment.initialize(self, compoundList)
+
+
+    def run(self):
+        Experiment.run(self)
+        datasetID = self.genepoolID
+        for (prog, settingsID) in self.programs:
+            try:
+                if prog.name() == "Locator":
+                    (settingName, settingData) = self.getSettingsID(settingsID)
+                    prog.setSettings(settingData)
+                    runID = self.setRun(prog.name(), datasetID, settingsID)
+                    tag = str(runID)
+                    prog.setTagID(tag)
+                    prog.run()
+                    theMotifs = prog.getMotifs()
+                    for mot in theMotifs:
+                        self.appendResults(mot)
+                else:
+                    self.mlog("Can only run Locate experiment with Locator program")
+            except:
+                self.mlog("Error running program %s with settings %s" % (prog, settingsID))
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