|
6
|
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 ## Interface for TablePathAdaptator
|
|
|
33 #
|
|
|
34 class ITablePathAdaptator (object):
|
|
|
35
|
|
|
36 ## Give the data contained in the table as a list of Path instances
|
|
|
37 #
|
|
|
38 # @return lPaths list of path instances
|
|
|
39 #
|
|
|
40 def getListOfAllPaths( self ):
|
|
|
41 pass
|
|
|
42
|
|
|
43 ## Give a list of Path instances having the same identifier
|
|
|
44 #
|
|
|
45 # @param id integer identifier number
|
|
|
46 # @return lPath a list of Path instances
|
|
|
47 #
|
|
|
48 # @warning old name was getPathList_from_num
|
|
|
49 #
|
|
|
50 def getPathListFromId( self, id ):
|
|
|
51 pass
|
|
|
52
|
|
|
53 ## Give a list of Path instances according to the given list of identifier numbers
|
|
|
54 #
|
|
|
55 # @param lId integer list
|
|
|
56 # @return lPath a list of Path instances
|
|
|
57 #
|
|
|
58 # @warning old name was getPathList_from_numlist
|
|
|
59 #
|
|
|
60 def getPathListFromIdList( self, lId ):
|
|
|
61 pass
|
|
|
62
|
|
|
63 ## Give a list of Path instances having the same given query name
|
|
|
64 #
|
|
|
65 # @param query string name of the query
|
|
|
66 # @return lPath a list of Path instances
|
|
|
67 #
|
|
|
68 # @warning old name was getPathList_from_query
|
|
|
69 #
|
|
|
70 def getPathListFromQuery( self, query ):
|
|
|
71 pass
|
|
|
72
|
|
|
73 ## Give a list with all the distinct identifiers corresponding to the query
|
|
|
74 #
|
|
|
75 # @param query string name of the query
|
|
|
76 # @return lId a list of integer
|
|
|
77 #
|
|
|
78 # @warning old name was getPathList_from_query
|
|
|
79 #
|
|
|
80 def getIdListFromQuery( self, query ):
|
|
|
81 pass
|
|
|
82
|
|
|
83 ## Give a list with all the distinct identifiers corresponding to the subject
|
|
|
84 #
|
|
|
85 # @param subject string name of the subject
|
|
|
86 # @return lId a list of integer
|
|
|
87 #
|
|
|
88 # @warning old name was getPathList_from_subject
|
|
|
89 #
|
|
|
90 def getIdListFromSubject( self, subject ):
|
|
|
91 pass
|
|
|
92
|
|
|
93 ## Insert a path instance
|
|
|
94 #
|
|
|
95 # @param obj a path instance
|
|
|
96 # @param delayed boolean indicating if the insert must be delayed
|
|
|
97 #
|
|
|
98 # @note data are inserted such that the query is always on the direct strand
|
|
|
99 #
|
|
|
100 # @warning old name was insAPath
|
|
|
101 #
|
|
|
102 def insert(self, obj, delayed = False):
|
|
|
103 pass
|
|
|
104
|
|
|
105 ## Insert a list of Path instances
|
|
|
106 #
|
|
|
107 # @param l a list of Path instances
|
|
|
108 # @param delayed boolean
|
|
|
109 #
|
|
|
110 # @warning old name was insPathList
|
|
|
111 #
|
|
|
112 def insertList(self, l, delayed = False):
|
|
|
113 pass
|
|
|
114
|
|
|
115 ## Give a list of the identifier number contained in the table
|
|
|
116 #
|
|
|
117 # @return l integer list
|
|
|
118 #
|
|
|
119 # @warning old name was getPath_num
|
|
|
120 #
|
|
|
121 def getIdList(self):
|
|
|
122 pass
|
|
|
123
|
|
|
124 ## Give a list of Path instances having the same given subject name
|
|
|
125 #
|
|
|
126 # @param subject string name of the subject
|
|
|
127 # @return lPath a list of Path instances
|
|
|
128 #
|
|
|
129 # @warning old name was getPath_num
|
|
|
130 #
|
|
|
131 def getPathListFromSubject( self, subject ):
|
|
|
132 pass
|
|
|
133
|
|
|
134 ## Give a list of the distinct subject names present in the table
|
|
|
135 #
|
|
|
136 # @return lDistinctTypeNames string list
|
|
|
137 #
|
|
|
138 # @warning old name was getListDistinctSubjectName
|
|
|
139 #
|
|
|
140 def getSubjectList(self):
|
|
|
141 pass
|
|
|
142
|
|
|
143 ## Give a list of the distinct query names present in the table
|
|
|
144 #
|
|
|
145 # @return lDistinctQueryNames string list
|
|
|
146 #
|
|
|
147 # @warning old name was getListDistinctQueryName
|
|
|
148 #
|
|
|
149 def getQueryList(self):
|
|
|
150 pass
|
|
|
151
|
|
|
152 ## Give a list of Set instance list from the path contained on a query name
|
|
|
153 #
|
|
|
154 # @param queryName string query name
|
|
|
155 # @return lSet list of set instance
|
|
|
156 #
|
|
|
157 def getSubjectListFromQuery (self, queryName):
|
|
|
158 pass
|
|
|
159
|
|
|
160 ## Give a list of Path instances with the given query and subject, both on direct strand
|
|
|
161 #
|
|
|
162 # @param query string query name
|
|
|
163 # @param subject string subject name
|
|
|
164 # @return lPaths list of path instances
|
|
|
165 #
|
|
|
166 # @warning old name was getListPathsWithDirectQueryDirectSubjectPerQuerySubject
|
|
|
167 #
|
|
|
168 def getPathListWithDirectQueryDirectSubjectFromQuerySubject( self, query, subject ):
|
|
|
169 pass
|
|
|
170
|
|
|
171 ## Give a list of Path instances with the given query on direct strand and the given subject on reverse strand
|
|
|
172 #
|
|
|
173 # @param query string query name
|
|
|
174 # @param subject string subject name
|
|
|
175 # @return lPaths list of path instances
|
|
|
176 #
|
|
|
177 # @warning old name was getListPathsWithDirectQueryReverseSubjectPerQuerySubject
|
|
|
178 #
|
|
|
179 def getPathListWithDirectQueryReverseSubjectFromQuerySubject( self, query, subject ):
|
|
|
180 pass
|
|
|
181
|
|
|
182 ## Give the number of Path instances with the given query name
|
|
|
183 #
|
|
|
184 # @param query string query name
|
|
|
185 # @return pathNb integer the number of Path instances
|
|
|
186 #
|
|
|
187 # @warning old name was getNbPaths_from_query
|
|
|
188 #
|
|
|
189 def getNbPathsFromQuery( self, query ):
|
|
|
190 pass
|
|
|
191
|
|
|
192 ## Give the number of Path instances with the given subject name
|
|
|
193 #
|
|
|
194 # @param subject string subject name
|
|
|
195 # @return pathNb integer the number of Path instances
|
|
|
196 #
|
|
|
197 # @warning old name was getNbPaths_from_subject
|
|
|
198 #
|
|
|
199 def getNbPathsFromSubject( self, subject ):
|
|
|
200 pass
|
|
|
201
|
|
|
202 ## Give the number of distinct path identifiers
|
|
|
203 #
|
|
|
204 # @return idNb integer the number of Path instances
|
|
|
205 #
|
|
|
206 # @warning old name was getNbAllPathsnums
|
|
|
207 #
|
|
|
208 def getNbIds( self ):
|
|
|
209 pass
|
|
|
210
|
|
|
211 ## Give the number of distinct path identifiers for a given subject
|
|
|
212 #
|
|
|
213 # subjectName string subject name
|
|
|
214 # @return idNb integer the number of Path instances
|
|
|
215 #
|
|
|
216 # @warning old name was getNbPathsnums_from_subject
|
|
|
217 #
|
|
|
218 def getNbIdsFromSubject( self, subjectName ):
|
|
|
219 pass
|
|
|
220
|
|
|
221 ## Give the number of distinct path identifiers for a given query
|
|
|
222 #
|
|
|
223 # @param queryName string query name
|
|
|
224 # @return idNb integer the number of Path instances
|
|
|
225 #
|
|
|
226 # @warning old name was getNbPathsnums_from_query
|
|
|
227 #
|
|
|
228 def getNbIdsFromQuery( self, queryName ):
|
|
|
229 pass
|
|
|
230
|
|
|
231 ## Give a list of Path instances overlapping a given region
|
|
|
232 #
|
|
|
233 # @param query string query name
|
|
|
234 # @param start integer start coordinate
|
|
|
235 # @param end integer end coordinate
|
|
|
236 # @return lPath list of Path instances
|
|
|
237 #
|
|
|
238 def getPathListOverlappingQueryCoord( self, query, start, end ):
|
|
|
239 pass
|
|
|
240
|
|
|
241 ## Give a list of Set instances overlapping a given region
|
|
|
242 #
|
|
|
243 # @param query string query name
|
|
|
244 # @param start integer start coordinate
|
|
|
245 # @param end integer end coordinate
|
|
|
246 # @return lSet list of Set instances
|
|
|
247 #
|
|
|
248 # @warning old name was getSetList_from_qcoord
|
|
|
249 #
|
|
|
250 def getSetListOverlappingQueryCoord(self, query, start, end):
|
|
|
251 pass
|
|
|
252
|
|
|
253 ## Give a list of Path instances included in a given query region
|
|
|
254 #
|
|
|
255 # @param query string query name
|
|
|
256 # @param start integer start coordinate
|
|
|
257 # @param end integer end coordinate
|
|
|
258 # @return lPaths list of Path instances
|
|
|
259 #
|
|
|
260 # @warning old name was getIncludedPathList_from_qcoord
|
|
|
261 #
|
|
|
262 def getPathListIncludedInQueryCoord( self, query, start, end ):
|
|
|
263 pass
|
|
|
264
|
|
|
265 ## Give a list of Set instances included in a given region
|
|
|
266 #
|
|
|
267 # @param query string query name
|
|
|
268 # @param start integer start coordinate
|
|
|
269 # @param end integer end coordinate
|
|
|
270 # @return lSet list of Set instances
|
|
|
271 #
|
|
|
272 # @warning old name was getInSetList_from_qcoord
|
|
|
273 #
|
|
|
274 def getSetListIncludedInQueryCoord(self, query, start, end):
|
|
|
275 pass
|
|
|
276
|
|
|
277 ## Give a a list of Path instances sorted by query coordinates
|
|
|
278 #
|
|
|
279 # @return lPaths list of Path instances
|
|
|
280 #
|
|
|
281 # @warning old name was getListOfPathsSortedByQueryCoord
|
|
|
282 #
|
|
|
283 def getPathListSortedByQueryCoord( self ):
|
|
|
284 pass
|
|
|
285
|
|
|
286 ## Give a a list of Path instances sorted by query coordinates for a given query
|
|
|
287 #
|
|
|
288 # @param queryName string query name
|
|
|
289 # @return lPaths list of Path instances
|
|
|
290 #
|
|
|
291 def getPathListSortedByQueryCoordFromQuery( self, queryName ):
|
|
|
292 pass
|
|
|
293
|
|
|
294 ## Give a list of path instances sorted by increasing E-value
|
|
|
295 #
|
|
|
296 # queryName string query name
|
|
|
297 # @return lPaths list of path instances
|
|
|
298 #
|
|
|
299 def getPathListSortedByIncreasingEvalueFromQuery( self, queryName ):
|
|
|
300 pass
|
|
|
301
|
|
|
302 ## Give a cumulative length of all paths (fragments) for a given subject name
|
|
|
303 #
|
|
|
304 # @param subjectName string subject name
|
|
|
305 # @return nb Cumulative length for all path
|
|
|
306 # @warning doesn't take into account the overlaps !!
|
|
|
307 # @warning old name was getCumulPathLength_from_subject
|
|
|
308 #
|
|
|
309 def getCumulLengthFromSubject( self, subjectName ):
|
|
|
310 pass
|
|
|
311
|
|
|
312 ## Give a list of the length of all chains of paths for a given subject name
|
|
|
313 #
|
|
|
314 # @param subjectName string name of the subject
|
|
|
315 # @return lChainLengths list of lengths per chain of paths
|
|
|
316 # @warning doesn't take into account the overlaps !!
|
|
|
317 # @warning old name was getListChainLength_from_subject
|
|
|
318 #
|
|
|
319 def getChainLengthListFromSubject( self, subjectName ):
|
|
|
320 pass
|
|
|
321
|
|
|
322 ## Give a list of identity of all chains of paths for a given subject name
|
|
|
323 #
|
|
|
324 # @param subjectName string name of the subject
|
|
|
325 # @return lChainIdentities list of identities per chain of paths
|
|
|
326 # @warning doesn't take into account the overlaps !!
|
|
|
327 # @warning old name was getListChainIdentity_from_subject
|
|
|
328 #
|
|
|
329 def getChainIdentityListFromSubject( self, subjectName ):
|
|
|
330 pass
|
|
|
331
|
|
|
332 ## Give a list of Path lists sorted by weighted identity.
|
|
|
333 #
|
|
|
334 # @param qry query name
|
|
|
335 # @return lChains list of chains
|
|
|
336 #
|
|
|
337 def getListOfChainsSortedByAscIdentityFromQuery( self, qry ):
|
|
|
338 pass
|
|
|
339
|
|
|
340 ## Give a list of the length of all paths for a given subject name
|
|
|
341 #
|
|
|
342 # @param subjectName string name of the subject
|
|
|
343 # @return lPathLengths list of lengths per path
|
|
|
344 # @warning doesn't take into account the overlaps !!
|
|
|
345 # @warning old name was getListPathLength_from_subject
|
|
|
346 #
|
|
|
347 def getPathLengthListFromSubject( self, subjectName ):
|
|
|
348 pass
|
|
|
349
|
|
|
350 ## Give a a list with all distinct identifiers for a given subject sorted in decreasing order according to the length of the chains
|
|
|
351 #
|
|
|
352 # @return lPathNums a list of paths Id
|
|
|
353 #
|
|
|
354 # @warning old name was getPathNumListSortedByDecreasingChainLengthFromSubject
|
|
|
355 #
|
|
|
356 def getIdListSortedByDecreasingChainLengthFromSubject( self, subjectName ):
|
|
|
357 pass
|
|
|
358
|
|
|
359 ## Give a list of Set instance list from the path contained on a query name
|
|
|
360 #
|
|
|
361 # @param query string query name
|
|
|
362 # @return lSet list of set instance
|
|
|
363 #
|
|
|
364 # @warning old name was getSetList_from_contig
|
|
|
365 #
|
|
|
366 def getSetListFromQuery(self, query):
|
|
|
367 pass
|
|
|
368
|
|
|
369 ## Delete path corresponding to a given identifier number
|
|
|
370 #
|
|
|
371 # @param id integer identifier number
|
|
|
372 #
|
|
|
373 # @warning old name was delPath_from_num
|
|
|
374 #
|
|
|
375 def deleteFromId(self,id):
|
|
|
376 pass
|
|
|
377
|
|
|
378 ## Delete path corresponding to a given list of identifier number
|
|
|
379 #
|
|
|
380 # @param lId list of identifier number
|
|
|
381 #
|
|
|
382 # @warning old name was delPath_from_numlist
|
|
|
383 #
|
|
|
384 def deleteFromIdList(self,lId):
|
|
|
385 pass
|
|
|
386
|
|
|
387 ## Join two path by changing id number of id1 and id2 path to the least of id1 and id2
|
|
|
388 #
|
|
|
389 # @param id1 integer path number
|
|
|
390 # @param id2 integer path number
|
|
|
391 # @return newId integer id used to join
|
|
|
392 #
|
|
|
393 # @warning old name was joinPath
|
|
|
394 #
|
|
|
395 def joinTwoPaths(self,id1,id2):
|
|
|
396 pass
|
|
|
397
|
|
|
398 ## Get a new id number
|
|
|
399 #
|
|
|
400 # @return newId integer new id
|
|
|
401 #
|
|
|
402 def getNewId(self):
|
|
|
403 pass
|
|
|
404
|
|
|
405 ## Test if table is empty
|
|
|
406 #
|
|
|
407 def isEmpty( self ):
|
|
|
408 pass
|
|
|
409
|
|
|
410 ## Create a 'pathRange' table from a 'path' table.
|
|
|
411 # The output table summarizes the information per identifier.
|
|
|
412 # The min and max value are taken.
|
|
|
413 # The identity is averaged over the fragments.
|
|
|
414 # It may overwrite an existing table.
|
|
|
415 #
|
|
|
416 # @param outTable string name of the output table
|
|
|
417 # @return outTable string Table which summarizes the information per identifier
|
|
|
418 #
|
|
|
419 def path2PathRange( self, outTable="" ):
|
|
|
420 pass
|
|
|
421
|
|
|
422 ## Return the number of times a given instance is present in the table
|
|
|
423 # The identifier is not considered,
|
|
|
424 # only coordinates, score, E-value and identity.
|
|
|
425 #
|
|
|
426 # @return nbOcc integer
|
|
|
427 #
|
|
|
428 def getNbOccurrences( self, iPath ):
|
|
|
429 pass
|
