Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/sql/TableMapAdaptator.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 | |
32 import sys | |
33 from commons.core.sql.TableAdaptator import TableAdaptator | |
34 from commons.core.sql.ITableMapAdaptator import ITableMapAdaptator | |
35 from commons.core.coord.Map import Map | |
36 from commons.core.coord.MapUtils import MapUtils | |
37 | |
38 | |
39 ## Adaptator for Map table | |
40 # | |
41 class TableMapAdaptator( TableAdaptator, ITableMapAdaptator ): | |
42 | |
43 ## Give a list of Map instances having a given seq name | |
44 # | |
45 # @param seqName string seq name | |
46 # @return lMap list of instances | |
47 # | |
48 def getListFromSeqName( self, seqName ): | |
49 sqlCmd = "SELECT * FROM %s" % (self._table) | |
50 colum2Get, type2Get, attr2Get = self._getTypeColumAttr2Get(seqName) | |
51 sqlCmd += " WHERE " + colum2Get | |
52 sqlCmd += " = " | |
53 sqlCmd = sqlCmd + type2Get | |
54 sqlCmd = sqlCmd % "'" + attr2Get + "'" | |
55 return self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) | |
56 | |
57 ## Give a list of Map instances overlapping a given region | |
58 # | |
59 # @param query string query name | |
60 # @param start integer start coordinate | |
61 # @param end integer end coordinate | |
62 # @return list map instances | |
63 # | |
64 def getListOverlappingCoord(self, query, start, end): | |
65 sqlCmd = 'select * from %s where chr="%s" and ((start between least(%d,%d) and greatest(%d,%d) or end between least(%d,%d) and greatest(%d,%d)) or (least(start,end)<=least(%d,%d) and greatest(start,end)>=greatest(%d,%d))) ;' % (self._table, query, start, end, start, end, start, end, start, end, start, end, start, end) | |
66 return self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) | |
67 | |
68 ## Give a list of Map instances having a given sequence name | |
69 # | |
70 # @param seqName string sequence name | |
71 # @return lMap list of instances | |
72 # | |
73 def getMapListFromSeqName(self, seqName): | |
74 lMap = self.getListFromSeqName( seqName ) | |
75 return lMap | |
76 | |
77 #TODO: Check getListFromSeqName method: uses name instead of seqname | |
78 # ## Give a list of Map instances having a given sequence name from list | |
79 # # | |
80 # # @param lSeqName string sequence name list | |
81 # # @return lMap list of instances | |
82 # # | |
83 # def getMapListFromSeqNameList(self, lSeqName): | |
84 # lMap = [] | |
85 # [lMap.extend(self.getListFromSeqName(seqName)) for seqName in lSeqName] | |
86 # return lMap | |
87 | |
88 ## Give a list of Map instances having a given chromosome | |
89 # | |
90 # @param chr string chromosome | |
91 # @return lMap list of instances | |
92 # | |
93 def getMapListFromChr(self, chr): | |
94 sqlCmd = "SELECT * FROM %s WHERE chr='%s'" % (self._table, chr) | |
95 lMap = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) | |
96 return lMap | |
97 | |
98 ## Give a list of the distinct seqName/chr present in the table | |
99 # | |
100 # @return lDistinctContigNames string list | |
101 # | |
102 def getSeqNameList(self): | |
103 sqlCmd = "SELECT DISTINCT chr FROM %s" % ( self._table ) | |
104 lDistinctContigNames = self._iDb.getStringListWithSQLCmd(sqlCmd) | |
105 return lDistinctContigNames | |
106 | |
107 ## Return a list of Set instances from a given sequence name | |
108 # | |
109 # @param seqName string sequence name | |
110 # @return lSets list of Set instances | |
111 # | |
112 def getSetListFromSeqName( self, seqName ): | |
113 lMaps = self.getListFromSeqName( seqName ) | |
114 lSets = MapUtils.mapList2SetList( lMaps ) | |
115 return lSets | |
116 | |
117 ## Give a map instances list overlapping a given region | |
118 # | |
119 # @param seqName string seq name | |
120 # @param start integer start coordinate | |
121 # @param end integer end coordinate | |
122 # @return lMap list of map instances | |
123 # | |
124 def getMapListOverlappingCoord(self, seqName, start, end): | |
125 lMap = self.getListOverlappingCoord(seqName, start, end) | |
126 return lMap | |
127 | |
128 ## Return a list of Set instances overlapping a given sequence | |
129 # | |
130 # @param seqName string sequence name | |
131 # @param start integer start coordinate | |
132 # @param end integer end coordinate | |
133 # @return lSet list of Set instances | |
134 # | |
135 def getSetListOverlappingCoord( self, seqName, start, end ): | |
136 lMaps = self.getListOverlappingCoord( seqName, start, end ) | |
137 lSets = MapUtils.mapList2SetList( lMaps ) | |
138 return lSets | |
139 | |
140 ## Give a dictionary which keys are Map names and values the corresponding Map instances | |
141 # | |
142 # @return dName2Maps dict which keys are Map names and values the corresponding Map instances | |
143 # | |
144 def getDictPerName( self ): | |
145 dName2Maps = {} | |
146 lMaps = self.getListOfAllMaps() | |
147 for iMap in lMaps: | |
148 if dName2Maps.has_key( iMap.name ): | |
149 if iMap == dName2Maps[ iMap.name ]: | |
150 continue | |
151 else: | |
152 msg = "ERROR: in table '%s' two different Map instances have the same name '%s'" % ( self._table, iMap.name ) | |
153 sys.stderr.write( "%s\n" % ( msg ) ) | |
154 sys.exit(1) | |
155 dName2Maps[ iMap.name ] = iMap | |
156 return dName2Maps | |
157 | |
158 ## Return a list of Map instances with all the data contained in the table | |
159 # | |
160 # @return lMaps list of Map instances | |
161 # | |
162 def getListOfAllMaps( self ): | |
163 sqlCmd = "SELECT * FROM %s" % ( self._table ) | |
164 lMaps = self._iDb.getObjectListWithSQLCmd( sqlCmd, self._getInstanceToAdapt ) | |
165 return lMaps | |
166 | |
167 ## Give the end of map as integer | |
168 # | |
169 # @return end integer the end of map | |
170 # | |
171 def getEndFromSeqName(self, seqName): | |
172 sqlCmd = "SELECT end FROM %s WHERE chr = '%s'" % (self._table, seqName) | |
173 end = self._iDb.getIntegerWithSQLCmd(sqlCmd) | |
174 return end | |
175 | |
176 def _getInstanceToAdapt(self): | |
177 iMap = Map() | |
178 return iMap | |
179 | |
180 def _getTypeColumAttr2Get(self, name): | |
181 colum2Get = 'name' | |
182 type2Get = '%s' | |
183 attr2Get = name | |
184 return colum2Get, type2Get, attr2Get | |
185 | |
186 def _getTypeAndAttr2Insert(self, map): | |
187 type2Insert = ("'%s'","'%s'","'%d'","'%d'") | |
188 attr2Insert = (map.name, map.seqname, map.start, map.end) | |
189 return type2Insert, attr2Insert | |
190 | |
191 def _escapeAntislash(self, obj): | |
192 obj.name = obj.name.replace("\\", "\\\\") | |
193 obj.seqname = obj.seqname.replace("\\", "\\\\") |