diff commons/pyRepetUnit/convCoord/ConvMapChr2Chunk.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/pyRepetUnit/convCoord/ConvMapChr2Chunk.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,64 @@
+from copy import deepcopy
+from commons.core.sql.TableMapAdaptator import TableMapAdaptator
+from commons.core.coord.Map import Map
+import os
+
+class ConvMapChr2Chunk(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)));"
+                            
+        iTMA = TableMapAdaptator(self._db, self._tablename)
+        chr_list = iTMA.getSeqNameList()
+
+        for chr in chr_list:        
+            mlist = iTMA.getMapListFromChr(chr)  
+            for m in mlist:
+                sql_cmd = str_mask%(m.seqname,m.getMin(),m.getMax(),m.getMin(),m.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_m = deepcopy(m)
+                    new_m.seqname = chunk.name
+ 
+                    if (m.start > chunk.start and m.start < chunk.end):
+                        new_m.start = m.start - chunk.start + 1 
+                    if (m.end > chunk.start and m.end < chunk.end):
+                        new_m.end = m.end - chunk.start + 1
+                                                   
+                    if m.isOnDirectStrand():
+                        if m.start <= chunk.start:
+                            new_m.start = 1
+                        if m.end >= chunk.end:
+                            new_m.end = chunk.end - chunk.start + 1
+                    else:
+                        if m.end <= chunk.start:
+                            new_m.end = 1
+                        if m.start >= chunk.end:
+                            new_m.start = chunk.end - chunk.start + 1
+                            
+                    new_m.write(fout)
+ 
+        fout.close()
+    
+        self._db.createTable(self._outtable, "map", temp_file)
+    
+        os.remove(temp_file)           
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