Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/sql/TableBinSetAdaptator.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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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.sql.TableSetAdaptator import TableSetAdaptator | |
32 from commons.core.coord.SetUtils import SetUtils | |
33 | |
34 ## Adaptator for Set tables with bin indexes | |
35 # | |
36 class TableBinSetAdaptator(TableSetAdaptator): | |
37 | |
38 ## constructor | |
39 # | |
40 # @param iDb DbMySql instance instance of DbMySql | |
41 # @param tableName string table name (default = "") | |
42 # | |
43 def __init__(self, iDb, tableName = ""): | |
44 TableSetAdaptator.__init__(self, iDb, tableName) | |
45 self._table_idx = "%s_idx" % (self._table) | |
46 | |
47 ## Insert a set instance in a set bin table | |
48 # | |
49 # @param iSet set instance an instance of set object | |
50 # @param delayed boolean an insert delayed or not | |
51 # | |
52 def insASetInSetAndBinTable(self, iSet, delayed = False): | |
53 self.insert(iSet, delayed) | |
54 iSet.seqname = iSet.seqname.replace("\\", "\\\\") | |
55 iSet.name = iSet.name.replace("\\", "\\\\") | |
56 bin = iSet.getBin() | |
57 max = iSet.getMax() | |
58 min = iSet.getMin() | |
59 strand = iSet.isOnDirectStrand() | |
60 sql_prefix = '' | |
61 if delayed: | |
62 sql_prefix = 'INSERT DELAYED INTO ' | |
63 else: | |
64 sql_prefix = 'INSERT INTO ' | |
65 sql_cmd = sql_prefix + '%s VALUES (%d,%f,"%s",%d,%d,%d)'\ | |
66 %(self._table_idx,\ | |
67 iSet.id,\ | |
68 bin,\ | |
69 iSet.seqname,\ | |
70 min,\ | |
71 max,\ | |
72 strand) | |
73 self._iDb.execute(sql_cmd) | |
74 | |
75 ## Delete set corresponding to a given identifier number in set and bin set table | |
76 # @param id integer identifier number | |
77 # @note old name was delSet_from_num | |
78 # | |
79 def deleteFromIdFromSetAndBinTable(self, id): | |
80 self.deleteFromId(id) | |
81 sql_cmd = 'delete from %s where path=%d' % (self._table_idx, id) | |
82 self._iDb.execute(sql_cmd) | |
83 | |
84 ## Delete path corresponding to a given list of identifier number | |
85 # | |
86 # @param lId integer list list of identifier number | |
87 # @note old name was delSet_from_listnum | |
88 # | |
89 def deleteFromListIdFromSetAndBinTable(self, lId): | |
90 if lId != []: | |
91 self.deleteFromIdList(lId) | |
92 sql_cmd = 'delete from %s where path=%d' % (self._table_idx, lId[0]) | |
93 for i in lId[1:]: | |
94 sql_cmd += " or path=%d" % (i) | |
95 self._iDb.execute(sql_cmd) | |
96 | |
97 ## Join two set by changing id number of id1 and id2 path | |
98 # to the least of id1 and id2 | |
99 # | |
100 # @param id1 integer id path number | |
101 # @param id2 integer id path number | |
102 # @return id integer new id | |
103 # @note old name was joinSet | |
104 # | |
105 def joinTwoSetsFromSetAndBinTable(self, id1, id2): | |
106 self.joinTwoSets(id1, id2) | |
107 if id1 < id2: | |
108 new_id = id1 | |
109 old_id = id2 | |
110 else: | |
111 new_id = id2 | |
112 old_id = id1 | |
113 sql_cmd = 'UPDATE %s SET path=%d WHERE path=%d'\ | |
114 % (self._table_idx, new_id, old_id) | |
115 self._iDb.execute(sql_cmd) | |
116 return new_id | |
117 | |
118 ## Get a new id number from set bin table | |
119 # | |
120 def getNewId(self): | |
121 sql_cmd = 'select max(path) from %s;' % (self._table_idx) | |
122 self._iDb.execute(sql_cmd) | |
123 max_id = self._iDb.fetchall()[0][0] | |
124 if max_id != None: | |
125 return int(max_id)+1 | |
126 else: | |
127 return 1 | |
128 | |
129 ## Get a set list instance between start and end parameters | |
130 # using the bin scheme | |
131 # | |
132 # @param seqName reference seq name | |
133 # @param start start coordinate | |
134 # @param end end coordinate | |
135 # @return lSet set list | |
136 # @note old name was getSetList_from_qcoord | |
137 # | |
138 def getSetListFromQueryCoord(self, seqName, start, end): | |
139 | |
140 min_coord = min(start,end) | |
141 max_coord = max(start,end) | |
142 | |
143 sql_cmd = 'select path from %s where contig="%s" and ('\ | |
144 % (self._table + "_idx", seqName) | |
145 for i in xrange(8, 2, -1): | |
146 bin_lvl = pow(10, i) | |
147 if int(start/bin_lvl) == int(end/bin_lvl): | |
148 bin = float(bin_lvl + (int(start / bin_lvl) / 1e10)) | |
149 sql_cmd += 'bin=%f' % (bin) | |
150 else: | |
151 bin1 = float(bin_lvl + (int(start / bin_lvl) / 1e10)) | |
152 bin2 = float(bin_lvl + (int(end /bin_lvl) / 1e10)) | |
153 sql_cmd += 'bin between %f and %f' % (bin1, bin2) | |
154 if bin_lvl != 1000: | |
155 sql_cmd += " or " | |
156 | |
157 sql_cmd += ") and min<=%d and max>=%d" % (max_coord, min_coord); | |
158 self._iDb.execute(sql_cmd) | |
159 res = self._iDb.fetchall() | |
160 lId = [] | |
161 for i in res: | |
162 lId.append(int(i[0])) | |
163 lSet = self.getSetListFromIdList(lId) | |
164 return lSet | |
165 | |
166 ## Get a set list instances strictly included between start and end parameters | |
167 # using the bin scheme | |
168 # | |
169 # @param seqName reference seq name | |
170 # @param start start coordinate | |
171 # @param end end coordinate | |
172 # @return lSet set list | |
173 # @note old name was getInSetList_from_qcoord | |
174 # @warning the implementation has been changed : I added the two first lines | |
175 # | |
176 def getSetListStrictlyIncludedInQueryCoord(self, contig, start, end): | |
177 min_coord = min(start,end) | |
178 max_coord = max(start,end) | |
179 lSet = self.getSetListFromQueryCoord(contig, start, end) | |
180 lSetStrictlyIncluded = [] | |
181 for iSet in lSet: | |
182 if iSet.getMin() > min_coord and \ | |
183 iSet.getMax() < max_coord: | |
184 lSetStrictlyIncluded.append(iSet) | |
185 | |
186 return lSetStrictlyIncluded | |
187 | |
188 ## Get a list of the identifier Id contained in the table bin | |
189 # | |
190 # @return lId list of int list of identifier | |
191 # @note old name was getSet_num | |
192 # | |
193 def getIdList(self): | |
194 sql_cmd = 'select distinct path from %s;' % (self._table_idx) | |
195 self._iDb.execute(sql_cmd) | |
196 res = self._iDb.fetchall() | |
197 lId = [] | |
198 for t in res: | |
199 lId.append(int(t[0])) | |
200 return lId | |
201 | |
202 ## Get a list of the query sequence name contained in the table bin | |
203 # | |
204 # @return lSeqName list of string list of query sequence name | |
205 # @note old name was getContig_name | |
206 # | |
207 def getSeqNameList(self): | |
208 sql_cmd = 'select distinct contig from %s;' % (self._table_idx) | |
209 self._iDb.execute(sql_cmd) | |
210 res = self._iDb.fetchall() | |
211 lSeqName = [] | |
212 for t in res: | |
213 lSeqName.append(t[0]) | |
214 return lSeqName | |
215 | |
216 ## Insert a Set list with the same new identifier in the table bin and set | |
217 # | |
218 # @note old name was insAddSetList | |
219 # | |
220 def insertListInSetAndBinTable(self, lSets, delayed = False): | |
221 id = self.getNewId() | |
222 SetUtils.changeIdInList( lSets, id ) | |
223 for iSet in lSets: | |
224 self.insASetInSetAndBinTable(iSet, delayed) | |
225 | |
226 ## Insert a set list instances In table Bin and Set and merge all overlapping sets | |
227 # | |
228 # @param lSets reference seq name | |
229 # @note old name was insMergeSetList | |
230 # | |
231 def insertListInSetAndBinTableAndMergeAllSets(self, lSets): | |
232 min, max = SetUtils.getListBoundaries(lSets) | |
233 oldLSet = self.getSetListFromQueryCoord(lSets[0].seqname, min, max) | |
234 oldQueryhash = SetUtils.getDictOfListsWithIdAsKey(oldLSet) | |
235 qhash = SetUtils.getDictOfListsWithIdAsKey(lSets) | |
236 for lNewSetById in qhash.values(): | |
237 found = False | |
238 for currentId, oldLsetById in oldQueryhash.items(): | |
239 if SetUtils.areSetsOverlappingBetweenLists(lNewSetById, oldLsetById): | |
240 oldLsetById.extend(lNewSetById) | |
241 oldLsetById = SetUtils.mergeSetsInList(oldLsetById) | |
242 self.deleteFromIdFromSetAndBinTable(currentId) | |
243 found = True | |
244 if not found: | |
245 self.insertListInSetAndBinTable(lNewSetById) | |
246 else: | |
247 id = self.getNewId() | |
248 SetUtils.changeIdInList(oldLsetById, id) | |
249 self.insertListInSetAndBinTable(oldLsetById) | |
250 | |
251 ## Insert a set list instances In table Bin and Set after removing all overlaps between database and lSets | |
252 # | |
253 # @param lSets reference seq name | |
254 # @note old name was insDiffSetList | |
255 # | |
256 def insertListInSetAndBinTableAndRemoveOverlaps(self, lSets): | |
257 min, max = SetUtils.getListBoundaries(lSets) | |
258 oldLSet = self.getSetListFromQueryCoord(lSets[0].seqname, min, max) | |
259 oldQueryHash = SetUtils.getDictOfListsWithIdAsKey(oldLSet) | |
260 newQueryHash = SetUtils.getDictOfListsWithIdAsKey(lSets) | |
261 for lNewSetById in newQueryHash.values(): | |
262 for lOldSetById in oldQueryHash.values(): | |
263 if SetUtils.areSetsOverlappingBetweenLists(lNewSetById, lOldSetById): | |
264 lNewSetById = SetUtils.getListOfSetWithoutOverlappingBetweenTwoListOfSet(lOldSetById, lNewSetById) | |
265 self.insertListInSetAndBinTable(lNewSetById) |