erange 4.0a dev release with integrated cistematic

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

diff --git a/cistematic/experiments/varyLength.py b/cistematic/experiments/varyLength.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.                                                               #
+###########################################################################
+#
+# a simple use of the experiment class
+from experiment import Experiment
+from analyzeMotifs import AnalyzeMotifs
+
+class VaryLength(Experiment, AnalyzeMotifs):
+    experimentType = "varyLength"
+
+
+    def setRange(self, step, uMin=0, uMax=0, dMin=0, dMax=0):
+        self.stepSize      = step
+        self.upstreamMin   = uMin
+        self.upstreamMax   = uMax + 1
+        self.downstreamMin = dMin
+        self.downstreamMax = dMax + 1
+
+
+    def run(self):
+        Experiment.run(self)
+
+        for downP in range(self.downstreamMin, self.downstreamMax, self.stepSize):
+            for upP in range(self.upstreamMin, self.upstreamMax, self.stepSize):
+                self.setSeqParameters(upP, downP)
+                # force reloading of the genepool
+                self.loadGenepool()
+                datasetID = self.genepoolID
+                fastaFile = self.createDataFile()
+                for (prog, settingsID) in self.programs:
+                    prog.inputFile(fastaFile)
+                    # reset setttings to orig settings, set new length, save settings
+                    prog.setSettings(self.settings[settingsID])
+                    prog.setSeqLength(str(upP + downP))
+                    newestSettingsID = self.setSettings(prog.getSettings())
+                    runID = self.setRun(prog.name(), datasetID, newestSettingsID)
+                    tag = str(runID)
+                    prog.setTagID(tag)
+                    prog.run()
+                    theMotifs = prog.getMotifs()
+                    for mot in theMotifs:
+                        self.results.append(mot)
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