--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/convCoord/ConvSetChr2Chunk.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,66 @@
+from copy import deepcopy
+from commons.core.sql.TableSetAdaptator import TableSetAdaptator
+from commons.core.coord.Map import Map
+from commons.core.coord.Set import Set
+import os
+
+class ConvSetChr2Chunk(object):
+
+    def __init__(self, db, table, chunk_table, outtable):
+        self._tablename = table
+        self._chunk_table = chunk_table
+        self._db = db
+        self._outtable = outtable
+        
+    def convert(self):
+        """
+        Convert a 'set' table format.
+        """
+        temp_file = str(os.getpid()) + ".on_chunk"
+        fout = open(temp_file,'w')
+
+        str_mask = "SELECT * FROM "+\
+            self._chunk_table + " WHERE chr='%s' AND ("+\
+            "(%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
+            " OR (%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
+            " OR (%d <= LEAST(start,end) AND %d >= GREATEST(start,end)));"
+                            
+        iTSA = TableSetAdaptator(self._db, self._tablename)
+        path_num_list = iTSA.getIdList()
+
+        for path_num in path_num_list:        
+            slist = iTSA.getSetListFromId(path_num)  
+            for r in slist:
+                sql_cmd = str_mask%(r.seqname,r.getMin(),r.getMax(),r.getMin(),r.getMax())
+                self._db.execute(sql_cmd)
+                res = self._db.fetchall()
+                for i in res:
+                    chunk = Map(i[0],i[1],int(i[2]),int(i[3]))
+                
+                    new_r = Set()
+                    new_r = deepcopy(r)
+                    new_r.seqname = chunk.name
+ 
+                    if (r.start > chunk.start and r.start < chunk.end):
+                        new_r.start = r.start - chunk.start + 1 
+                    if (r.end > chunk.start and r.end < chunk.end):
+                        new_r.end = r.end - chunk.start + 1
+                                                   
+                    if r.isOnDirectStrand():
+                        if r.start <= chunk.start:
+                            new_r.start = 1
+                        if r.end >= chunk.end:
+                            new_r.end = chunk.end - chunk.start + 1
+                    else:
+                        if r.end <= chunk.start:
+                            new_r.end = 1
+                        if r.start >= chunk.end:
+                            new_r.start = chunk.end - chunk.start + 1
+                            
+                    new_r.write(fout)
+ 
+        fout.close()
+    
+        self._db.createTable(self._outtable, "set", temp_file)
+    
+        os.remove(temp_file)           
\ No newline at end of file