Mercurial > repos > yufei-luo > s_mart

comparison commons/pyRepetUnit/convCoord/ConvPathChr2Chunk.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.TablePathAdaptator import TablePathAdaptator
3 from commons.core.coord.PathUtils import PathUtils
4 from commons.core.coord.Map import Map
5 from commons.core.coord.Path import Path
6 import os
7
8 class ConvPathChr2Chunk(object):
9
10 def __init__(self, db, table, chunk_table, outtable):
11 self._tablename = table
12 self._chunk_table = chunk_table
13 self._db = db
14 self._outtable = outtable
15
16 def convert(self):
17 """
18 Convert a 'path' table format.
19 """
20 temp_file = str(os.getpid()) + ".on_chunk"
21 fout = open(temp_file,'w')
22
23 str_mask = "SELECT * FROM "+\
24 self._chunk_table + " WHERE chr='%s' AND ("+\
25 "(%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
26 " OR (%d BETWEEN LEAST(start,end) AND GREATEST(start,end))"+\
27 " OR (%d <= LEAST(start,end) AND %d >= GREATEST(start,end)));"
28
29 iTPA = TablePathAdaptator(self._db, self._tablename)
30 path_num_list = iTPA.getIdList()
31
32 for path_num in path_num_list:
33 slist = iTPA.getPathListFromId(path_num)
34 for r in slist:
35 r_min, r_max = PathUtils.getQueryMinMaxFromPathList([r])
36 sql_cmd = str_mask%(r.range_query.seqname,r_min,r_max,r_min,r_max)
37 self._db.execute(sql_cmd)
38 res = self._db.fetchall()
39 for i in res:
40 chunk = Map(i[0],i[1],int(i[2]),int(i[3]))
41
42 new_r = Path()
43 new_r = deepcopy(r)
44 new_r.range_query.seqname = chunk.name
45
46 if (r.range_query.start > chunk.start and r.range_query.start < chunk.end):
47 new_r.range_query.start = r.range_query.start - chunk.start + 1
48 if (r.range_query.end > chunk.start and r.range_query.end < chunk.end):
49 new_r.range_query.end = r.range_query.end - chunk.start + 1
50
51 if r.range_query.isOnDirectStrand():
52 if r.range_query.start <= chunk.start:
53 new_r.range_query.start = 1
54 if r.range_query.end >= chunk.end:
55 new_r.range_query.end = chunk.end - chunk.start + 1
56 else:
57 if r.range_query.end <= chunk.start:
58 new_r.range_query.end = 1
59 if r.range_query.start >= chunk.end:
60 new_r.range_query.start = chunk.end - chunk.start + 1
61
62 new_r.write(fout)
63
64 fout.close()
65
66 self._db.createTable(self._outtable, "path", temp_file)
67
68 os.remove(temp_file)