Mercurial > repos > yufei-luo > s_mart

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
equal deleted inserted replaced
30:5677346472b5 31:0ab839023fe4
1 from copy import deepcopy
2 from commons.core.sql.TableMapAdaptator import TableMapAdaptator
3 from commons.core.coord.Map import Map
4 import os
5
6 class ConvMapChr2Chunk(object):
7
8 def __init__(self, db, table, chunk_table, outtable):
9 self._tablename = table
10 self._chunk_table = chunk_table
11 self._db = db
12 self._outtable = outtable
13
14 def convert(self):
15 """
16 Convert a 'set' table format.
17 """
18 temp_file=str(os.getpid()) + ".on_chunk"
19 fout=open(temp_file,'w')
20
21 str_mask = "SELECT * FROM "+\
22 self._chunk_table + " WHERE chr='%s' AND ("+\
23 "(%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
24 " OR (%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
25 " OR (%d <= LEAST(start,end) AND %d >= GREATEST(start,end)));"
26
27 iTMA = TableMapAdaptator(self._db, self._tablename)
28 chr_list = iTMA.getSeqNameList()
29
30 for chr in chr_list:
31 mlist = iTMA.getMapListFromChr(chr)
32 for m in mlist:
33 sql_cmd = str_mask%(m.seqname,m.getMin(),m.getMax(),m.getMin(),m.getMax())
34 self._db.execute(sql_cmd)
35 res = self._db.fetchall()
36 for i in res:
37 chunk = Map(i[0],i[1],int(i[2]),int(i[3]))
38
39 new_m = deepcopy(m)
40 new_m.seqname = chunk.name
41
42 if (m.start > chunk.start and m.start < chunk.end):
43 new_m.start = m.start - chunk.start + 1
44 if (m.end > chunk.start and m.end < chunk.end):
45 new_m.end = m.end - chunk.start + 1
46
47 if m.isOnDirectStrand():
48 if m.start <= chunk.start:
49 new_m.start = 1
50 if m.end >= chunk.end:
51 new_m.end = chunk.end - chunk.start + 1
52 else:
53 if m.end <= chunk.start:
54 new_m.end = 1
55 if m.start >= chunk.end:
56 new_m.start = chunk.end - chunk.start + 1
57
58 new_m.write(fout)
59
60 fout.close()
61
62 self._db.createTable(self._outtable, "map", temp_file)
63
64 os.remove(temp_file)