view commons/pyRepetUnit/convCoord/ConvSetChr2Chunk.py @ 18:94ab73e8a190

Uploaded

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)