erange 4.0a dev release with integrated cistematic

[erange.git] / cistematic / programs / locator.py

diff --git a/cistematic/programs/locator.py b/cistematic/programs/locator.py
new file mode 100644 (file)
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+++ b/cistematic/programs/locator.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.                                                               #
+###########################################################################
+#
+# locator.py
+from cistematic.programs import Program
+from cistematic.core.motif import Motif
+
+class Locator(Program):
+    motifs = []
+    consensus = "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
+    identifier = "DEFAULT"
+    PWM = []
+    seqs = []
+    motFile = ""
+
+
+    def getSettings(self):
+        return (self.consensus, self.identifier, self.PWM, self.seqs, self.motFile)
+
+
+    def setSettings(self, settings):
+        self.motifs = []
+        progsettings = ""
+        commSettings = "progsettings = %s" % str(settings)
+        exec commSettings
+        (self.consensus, self.identifier, self.PWM, self.seqs, self.motFile) = progsettings
+
+
+    def setGenExpOptions(self, optionArray):
+        for option in optionArray:
+            (optionTag, optionValue) = option.split(":")
+            if optionTag == "consensus":
+                self.setConsensus(optionValue)
+
+            if optionTag == "identifier":
+                self.setID(optionValue)
+
+
+    def setConsensus(self, cons):
+        self.consensus = cons
+
+
+    def setID(self, ident):
+        self.identifier = ident
+
+
+    def setPWM(self, aPWM):
+        self.PWM[self.identifier] = aPWM
+
+
+    def useMotifFile(self, mFile):
+        self.motFile = mFile
+
+
+    def run(self):
+        pass
+
+
+    def getMotifs(self):
+        self.motifs = []
+        if self.motFile != "":
+            motif = Motif("%s-LOC-%s" % (self.tagID, self.identifier), motifFile=self.motFile)
+            self.motifs.append(motif)
+        else:
+            motif = Motif("%s-LOC-%s" % (self.tagID, self.identifier), self.consensus, self.PWM, self.seqs)
+            self.motifs.append(motif)
+
+        return self.motifs
\ No newline at end of file