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comparison commons/core/sql/TableBinPathAdaptator.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
1 # Copyright INRA (Institut National de la Recherche Agronomique)
2 # http://www.inra.fr
3 # http://urgi.versailles.inra.fr
4 #
5 # This software is governed by the CeCILL license under French law and
6 # abiding by the rules of distribution of free software. You can use,
7 # modify and/ or redistribute the software under the terms of the CeCILL
8 # license as circulated by CEA, CNRS and INRIA at the following URL
9 # "http://www.cecill.info".
10 #
11 # As a counterpart to the access to the source code and rights to copy,
12 # modify and redistribute granted by the license, users are provided only
13 # with a limited warranty and the software's author, the holder of the
14 # economic rights, and the successive licensors have only limited
15 # liability.
16 #
17 # In this respect, the user's attention is drawn to the risks associated
18 # with loading, using, modifying and/or developing or reproducing the
19 # software by the user in light of its specific status of free software,
20 # that may mean that it is complicated to manipulate, and that also
21 # therefore means that it is reserved for developers and experienced
22 # professionals having in-depth computer knowledge. Users are therefore
23 # encouraged to load and test the software's suitability as regards their
24 # requirements in conditions enabling the security of their systems and/or
25 # data to be ensured and, more generally, to use and operate it in the
26 # same conditions as regards security.
27 #
28 # The fact that you are presently reading this means that you have had
29 # knowledge of the CeCILL license and that you accept its terms.
30
31 from commons.core.coord.Range import getIdx
32 from commons.core.sql.TablePathAdaptator import TablePathAdaptator
33 from commons.core.coord.PathUtils import PathUtils
34
35 ## Bin Adaptator for a path table.
36 #
37 class TableBinPathAdaptator(TablePathAdaptator):
38
39
40 ## Constructor
41 #
42 # @param db db instance
43 # @param tableName string table name (default = "")
44 #
45 def __init__(self, db, tableName = ""):
46 TablePathAdaptator.__init__(self, db, tableName)
47 self._table_idx = "%s_idx" % (self._table)
48
49 ## Insert a path instance
50 #
51 # @param path a path instance
52 # @param delayed boolean indicating if the insert must be delayed (default = false)
53 #
54 def insert( self, path, delayed = False ):
55 TablePathAdaptator.insert(self, path, delayed)
56 self._escapeAntislash(path)
57 idx = path.range_query.findIdx()
58 max = path.range_query.getMax()
59 min = path.range_query.getMin()
60 strand = path.range_query.isOnDirectStrand()
61 if delayed:
62 sql_cmd = 'INSERT DELAYED INTO %s VALUES (%d,%d,"%s",%d,%d,%d)'\
63 % (self._table_idx,\
64 path.id,\
65 idx,\
66 path.range_query.seqname,\
67 min,\
68 max,\
69 strand)
70 else:
71 sql_cmd = 'INSERT INTO %s VALUES (%d,%d,"%s",%d,%d,%d)'\
72 % (self._table_idx,\
73 path.id,\
74 idx,\
75 path.range_query.seqname,\
76 min,\
77 max,\
78 strand)
79
80 self._iDb.execute(sql_cmd)
81
82 ## Return a path instances list included in a given region using the bin scheme
83 #
84 # @param contig string contig name
85 # @param start integer start coordinate
86 # @param end integer end coordinate
87 # @return lOutPath a path instances list
88 #
89 def getPathListIncludedInQueryCoord(self, contig, start, end):
90 min_coord = min(start, end)
91 max_coord = max(start, end)
92 lpath = self.getChainListOverlappingQueryCoord(contig, start, end)
93 lOutPath = []
94 for i in lpath:
95 if i.range_query.getMin() > min_coord and \
96 i.range_query.getMax() < max_coord:
97 lOutPath.append(i)
98
99 return lOutPath
100
101 ## Return a path instances list overlapping (and included) in a given region using the bin scheme
102 #
103 # @param contig string contig name
104 # @param start integer start coordinate
105 # @param end integer end coordinate
106 # @return lOutPath a path instances list
107 #
108 def getPathListOverlappingQueryCoord(self, contig, start, end):
109 min_coord = min(start, end)
110 max_coord = max(start, end)
111 lpath = self.getChainListOverlappingQueryCoord(contig, start, end)
112 lOutPath = []
113 for i in lpath:
114 if ((i.range_query.getMin() <= min_coord and i.range_query.getMax() >= min_coord) or \
115 (i.range_query.getMin() >= min_coord and i.range_query.getMin() <= max_coord) or \
116 (i.range_query.getMin() <= min_coord and i.range_query.getMax() >= max_coord) or \
117 (i.range_query.getMin() >= min_coord and i.range_query.getMax() <= max_coord)) and \
118 (i.range_query.getSeqname() == contig):
119 lOutPath.append(i)
120
121 return lOutPath
122
123 ## Return a path instances list chain (by Id and Coord in chr) list overlapping a given region using the bin scheme
124 #
125 # @param contig string contig name
126 # @param start integer start coordinate
127 # @param end integer end coordinate
128 # @return lpath a path instances list
129 #
130 def getChainListOverlappingQueryCoord(self, contig, start, end):
131 min_coord = min(start, end)
132 max_coord = max(start, end)
133 sql_cmd = 'select distinct path from %s where contig="%s" and ('\
134 % (self._table + "_idx", contig)
135
136 for bin_lvl in xrange(6, 2, -1):
137 if getIdx(start,bin_lvl) == getIdx(end, bin_lvl):
138 idx = getIdx(start, bin_lvl)
139 sql_cmd += 'idx=%d' % (idx)
140 else:
141 idx1 = getIdx(min_coord, bin_lvl)
142 idx2 = getIdx(max_coord, bin_lvl)
143 sql_cmd += 'idx between %d and %d' % (idx1, idx2)
144 if bin_lvl > 3:
145 sql_cmd += " or "
146
147 sql_cmd += ") and min<=%d and max>=%d;" % (max_coord, min_coord)
148
149
150 self._iDb.execute(sql_cmd)
151 res = self._iDb.fetchall()
152 lnum = []
153 for i in res:
154 lnum.append( int(i[0]) )
155 lpath = self.getPathListFromIdList(lnum)
156 return lpath
157
158 ## Delete path corresponding to a given identifier number
159 #
160 # @param num integer identifier number
161 #
162 def deleteFromId(self, num):
163 TablePathAdaptator.deleteFromId(self, num)
164 sqlCmd='delete from %s where path=%d;' % (self._table_idx, num)
165 self._iDb.execute(sqlCmd)
166
167 ## Delete path corresponding to a given list of identifier number
168 #
169 # @param lNum list list of integer identifier number
170 #
171 def deleteFromIdList(self, lNum):
172 if lNum == []:
173 return
174 TablePathAdaptator.deleteFromIdList(self, lNum)
175 sqlCmd = 'delete from %s where path=%d' % (self._table_idx, lNum[0])
176 for i in lNum[1:]:
177 sqlCmd += " or path=%d" % (i)
178 sqlCmd += ";"
179 self._iDb.execute(sqlCmd)
180
181 ## Join two path by changing id number of id1 and id2 path to the least of id1 and id2
182 #
183 # @param id1 integer id path number
184 # @param id2 integer id path number
185 # @return newId integer minimum of id1 id2
186 # @note this method modify the ID even if this one not existing in the path table
187 #
188 def joinTwoPaths(self, id1, id2):
189 TablePathAdaptator.joinTwoPaths(self, id1, id2)
190 if id1 < id2:
191 newId = id1
192 oldId = id2
193 else:
194 newId = id2
195 oldId = id1
196 sqlCmd = 'UPDATE %s SET path=%d WHERE path=%d' % (self._table_idx, newId, oldId)
197 self._iDb.execute(sqlCmd)
198 return newId
199
200 ## Get a new id number
201 #
202 # @return newId integer max Id in path table + 1
203 #
204 def getNewId(self):
205 sqlCmd = 'select max(path) from %s;' % (self._table_idx)
206 self._iDb.execute(sqlCmd)
207 maxId = self._iDb.fetchall()[0][0]
208 if maxId == None:
209 maxId = 0
210 newId = int(maxId) + 1
211 return newId
212
213 ## Give a list of Set instances included in a given region
214 #
215 # @param query string query name
216 # @param start integer start coordinate
217 # @param end integer end coordinate
218 # @return lSet list of Set instances
219 #
220 def getSetListIncludedInQueryCoord(self, query, start, end):
221 lPath=self.getPathListIncludedInQueryCoord(query, start, end)
222 lSet = PathUtils.getSetListFromQueries(lPath)
223 return lSet
224
225 ## Give a list of Set instances overlapping a given region
226 #
227 # @param query string query name
228 # @param start integer start coordinate
229 # @param end integer end coordinate
230 # @return lSet list of Set instances
231 #
232 def getSetListOverlappingQueryCoord(self, query, start, end):
233 lPath = self.getPathListOverlappingQueryCoord(query, start, end)
234 lSet = PathUtils.getSetListFromQueries(lPath)
235 return lSet
236
237 ## Give a list of identifiers contained in the table
238 #
239 # @return lId integer list
240 #
241 def getIdList(self):
242 sqlCmd = "SELECT DISTINCT path from %s;" % (self._table_idx)
243 lId = self._iDb.getIntegerListWithSQLCmd( sqlCmd )
244 return lId
245
246 ## Give a list of the distinct query names present in the table
247 #
248 # @return lDistinctQueryNames string list
249 #
250 def getQueryList(self):
251 lDistinctQueryNames = self._getDistinctTypeNamesList("query")
252 return lDistinctQueryNames
253
254 def _getDistinctTypeNamesList( self, type ):
255 sqlCmd = "SELECT DISTINCT contig FROM %s" % ( self._table_idx )
256 lDistinctTypeNames = self._iDb.getStringListWithSQLCmd(sqlCmd)
257 return lDistinctTypeNames