--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/structure/Sequence.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,184 @@
+#
+# Copyright INRA-URGI 2009-2010
+# 
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software. You can use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+# 
+# As a counterpart to the access to the source code and rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty and the software's author, the holder of the
+# economic rights, and the successive licensors have only limited
+# liability.
+# 
+# In this respect, the user's attention is drawn to the risks associated
+# with loading, using, modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean that it is complicated to manipulate, and that also
+# therefore means that it is reserved for developers and experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and, more generally, to use and operate it in the
+# same conditions as regards security.
+# 
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+#
+import sys
+import re
+from commons.core.seq.Bioseq import Bioseq
+
+reverseComplementString = {
+    "A": "T",
+    "C": "G",
+    "G": "C",
+    "T": "A",
+    "U": "A",
+    "M": "K",
+    "R": "Y",
+    "W": "W",
+    "S": "S",
+    "Y": "R",
+    "K": "M",
+    "V": "B",
+    "H": "D",
+    "D": "H",
+    "B": "V",
+    "N": "N",
+    "a": "t",
+    "c": "g",
+    "g": "c",
+    "t": "a",
+    "u": "a",
+    "m": "k",
+    "r": "y",
+    "w": "w",
+    "s": "s",
+    "y": "r",
+    "k": "m",
+    "v": "b",
+    "h": "d",
+    "d": "h",
+    "b": "v",
+    "n": "n"
+}
+
+class Sequence(Bioseq):
+    """A class that codes for a sequence"""
+
+    def __init__(self, name = "", sequence = ""):
+        super(Sequence, self).__init__(name, sequence)
+        self.name            = self.header        
+        self.quality         = None
+        self.chunkedSequence = None
+        self.chunkedQuality  = None
+        self.integerQuality  = False
+
+    def setName(self, name=""):
+        super(Sequence, self).setHeader(name)
+            
+    def getName(self):
+        return self.getHeader()
+    
+    def setSequence(self, seq=""):
+        super(Sequence, self).setSequence(seq)
+
+    def setQuality(self, quality):
+        if quality == None:
+            self.quality = None
+            return
+        if " " in quality:
+            self.quality        = quality.split()
+            self.integerQuality = True
+        else:
+            self.quality = list(quality)
+        
+    def getQuality(self):
+        if self.quality == None:
+            return None
+        if self.integerQuality:
+            return " ".join(self.quality)
+        return "".join(self.quality)
+    
+    def getSize(self):
+        return len(self.getSequence())
+
+
+    def copy(self, sequence):
+        self.setName(sequence.getName())
+        self.setSequence(sequence.getSequence())
+        self.setQuality(sequence.getQuality())
+        self.chunkedSequence = None
+        self.chunkedQuality  = None
+
+
+    def chunkSequence(self):
+        self.chunkedSequence = []
+        for i in range (0, self.getSize() / 60 + 1):
+            self.chunkedSequence.append(self.getSequence()[i * 60 : min(self.getSize(), (i+1) * 60)])
+        if self.quality != None:
+            self.chunkedQuality = []
+            for i in range (0, self.getSize() / 60 + 1):
+                self.chunkedQuality.append(self.quality[i * 60 : min(self.getSize(), (i+1) * 60)])
+
+    def concatenate(self, seq):
+        sequence  = self.getSequence()
+        sequence += seq.getSequence()
+        self.setSequence(sequence)
+        if self.quality != None:
+            sep = " " if self.integerQuality else ""
+            self.setQuality(self.getQuality() + sep + seq.getQuality())
+        self.chunkedSequence = None
+        self.chunkedQuality  = None
+        
+
+    def printFasta(self):
+        if self.chunkedSequence == None:
+            self.chunkSequence()
+        return ">%s\n%s\n" % (self.getHeader(), "\n".join(self.chunkedSequence))
+
+
+    def printFastq(self):
+        if self.chunkedSequence == None:
+            self.chunkSequence()
+        return "@%s\n%s\n+%s\n%s\n" % (self.getHeader(), self.getSequence(), self.getHeader(), self.getQuality())
+
+
+    def reverseComplement(self):
+        seq = ""
+        self.chunkedSequence = None
+        self.chunkedQuality  = None
+        for i in range(0, self.getSize()):
+            char = self.getSequence()[i:i+1]
+            if char not in reverseComplementString:
+                sys.exit("Cannot understand character %s from string %s" % (char, self.getSequence()))
+            seq = "%s%s" % (reverseComplementString[char], seq)
+        self.setSequence(seq)
+        if self.quality != None:
+            self.quality = self.quality[::-1]
+        
+        
+    def containsAmbiguousNucleotides(self):
+        m = re.search("[^ACGTUacgtu]", self.getSequence())
+        if m != None:
+            return True
+        return False
+    
+    
+    def shrinkToFirstNucleotides(self, nbNucleotides):
+        self.chunkedSequence = None
+        self.chunkedQuality  = None
+        self.setSequence(self.getSequence()[0:nbNucleotides])
+        if self.quality != None:
+            self.quality = self.quality[0:nbNucleotides]
+    
+    
+    def shrinkToLastNucleotides(self, nbNucleotides):
+        self.chunkedSequence = None
+        self.chunkedQuality  = None
+        self.setSequence(self.getSequence()[-nbNucleotides:])
+        if self.quality != None:
+            self.quality = self.quality[-nbNucleotides:]