Mercurial > repos > yufei-luo > s_mart

comparison commons/pyRepetUnit/convCoord/ConvSetChr2Chunk.py @ 31:0ab839023fe4

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
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30:5677346472b5 31:0ab839023fe4
1 from copy import deepcopy
2 from commons.core.sql.TableSetAdaptator import TableSetAdaptator
3 from commons.core.coord.Map import Map
4 from commons.core.coord.Set import Set
5 import os
6
7 class ConvSetChr2Chunk(object):
8
9 def __init__(self, db, table, chunk_table, outtable):
10 self._tablename = table
11 self._chunk_table = chunk_table
12 self._db = db
13 self._outtable = outtable
14
15 def convert(self):
16 """
17 Convert a 'set' table format.
18 """
19 temp_file = str(os.getpid()) + ".on_chunk"
20 fout = open(temp_file,'w')
21
22 str_mask = "SELECT * FROM "+\
23 self._chunk_table + " WHERE chr='%s' AND ("+\
24 "(%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
25 " OR (%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
26 " OR (%d <= LEAST(start,end) AND %d >= GREATEST(start,end)));"
27
28 iTSA = TableSetAdaptator(self._db, self._tablename)
29 path_num_list = iTSA.getIdList()
30
31 for path_num in path_num_list:
32 slist = iTSA.getSetListFromId(path_num)
33 for r in slist:
34 sql_cmd = str_mask%(r.seqname,r.getMin(),r.getMax(),r.getMin(),r.getMax())
35 self._db.execute(sql_cmd)
36 res = self._db.fetchall()
37 for i in res:
38 chunk = Map(i[0],i[1],int(i[2]),int(i[3]))
39
40 new_r = Set()
41 new_r = deepcopy(r)
42 new_r.seqname = chunk.name
43
44 if (r.start > chunk.start and r.start < chunk.end):
45 new_r.start = r.start - chunk.start + 1
46 if (r.end > chunk.start and r.end < chunk.end):
47 new_r.end = r.end - chunk.start + 1
48
49 if r.isOnDirectStrand():
50 if r.start <= chunk.start:
51 new_r.start = 1
52 if r.end >= chunk.end:
53 new_r.end = chunk.end - chunk.start + 1
54 else:
55 if r.end <= chunk.start:
56 new_r.end = 1
57 if r.start >= chunk.end:
58 new_r.start = chunk.end - chunk.start + 1
59
60 new_r.write(fout)
61
62 fout.close()
63
64 self._db.createTable(self._outtable, "set", temp_file)
65
66 os.remove(temp_file)