1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
|
---bad precedence: change customed type name
---drop here to remove old function
--DROP TYPE feature_by_cvt_type CASCADE;
--DROP TYPE fxgsfids_type CASCADE;
--DROP TYPE feature_by_fx_type CASCADE;
CREATE TYPE feature_by_fx_type AS (
feature_id INTEGER,
depth INT
);
CREATE OR REPLACE FUNCTION get_sub_feature_ids(text) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
sql alias for $1;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
FOR myrc IN EXECUTE sql LOOP
FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP
RETURN NEXT myrc2;
END LOOP;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
CREATE OR REPLACE FUNCTION get_up_feature_ids(text) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
sql alias for $1;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
FOR myrc IN EXECUTE sql LOOP
FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP
RETURN NEXT myrc2;
END LOOP;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
CREATE OR REPLACE FUNCTION get_feature_ids(text) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
sql alias for $1;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
myrc3 feature_by_fx_type%ROWTYPE;
BEGIN
FOR myrc IN EXECUTE sql LOOP
RETURN NEXT myrc;
FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP
RETURN NEXT myrc2;
END LOOP;
FOR myrc3 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP
RETURN NEXT myrc3;
END LOOP;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
root alias for $1;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
FOR myrc IN SELECT DISTINCT subject_id AS feature_id FROM feature_relationship WHERE object_id = root LOOP
RETURN NEXT myrc;
FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id) LOOP
RETURN NEXT myrc2;
END LOOP;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
CREATE OR REPLACE FUNCTION get_up_feature_ids(integer) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
leaf alias for $1;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
FOR myrc IN SELECT DISTINCT object_id AS feature_id FROM feature_relationship WHERE subject_id = leaf LOOP
RETURN NEXT myrc;
FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id) LOOP
RETURN NEXT myrc2;
END LOOP;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
CREATE OR REPLACE FUNCTION get_sub_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
root alias for $1;
depth alias for $2;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
FOR myrc IN SELECT DISTINCT subject_id AS feature_id, depth FROM feature_relationship WHERE object_id = root LOOP
RETURN NEXT myrc;
FOR myrc2 IN SELECT * FROM get_sub_feature_ids(myrc.feature_id,depth+1) LOOP
RETURN NEXT myrc2;
END LOOP;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
--- depth is reversed and meanless when union with results from get_sub_feature_ids
CREATE OR REPLACE FUNCTION get_up_feature_ids(integer, integer) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
leaf alias for $1;
depth alias for $2;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
FOR myrc IN SELECT DISTINCT object_id AS feature_id, depth FROM feature_relationship WHERE subject_id = leaf LOOP
RETURN NEXT myrc;
FOR myrc2 IN SELECT * FROM get_up_feature_ids(myrc.feature_id,depth+1) LOOP
RETURN NEXT myrc2;
END LOOP;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
--- children feature ids only (not include itself--parent) for SO type and range (src)
CREATE OR REPLACE FUNCTION get_sub_feature_ids_by_type_src(cvterm.name%TYPE,feature.uniquename%TYPE,char(1)) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
gtype alias for $1;
src alias for $2;
is_an alias for $3;
query text;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id)
INNER join featureloc fl
ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id)
WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src)
|| '' AND f.is_analysis = '' || quote_literal(is_an) || '';'';
IF (STRPOS(gtype, ''%'') > 0) THEN
query := ''SELECT DISTINCT f.feature_id FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id)
INNER join featureloc fl
ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id)
WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src)
|| '' AND f.is_analysis = '' || quote_literal(is_an) || '';'';
END IF;
FOR myrc IN SELECT * FROM get_sub_feature_ids(query) LOOP
RETURN NEXT myrc;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
--- by SO type, usefull for tRNA, ncRNA, etc
CREATE OR REPLACE FUNCTION get_feature_ids_by_type(cvterm.name%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
gtype alias for $1;
is_an alias for $2;
query TEXT;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
query := ''SELECT DISTINCT f.feature_id
FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name = '' || quote_literal(gtype) ||
'' AND f.is_analysis = '' || quote_literal(is_an) || '';'';
IF (STRPOS(gtype, ''%'') > 0) THEN
query := ''SELECT DISTINCT f.feature_id
FROM feature f, cvterm t WHERE t.cvterm_id = f.type_id AND t.name like ''
|| quote_literal(gtype) || '' AND f.is_analysis = '' || quote_literal(is_an) || '';'';
END IF;
FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
RETURN NEXT myrc;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
CREATE OR REPLACE FUNCTION get_feature_ids_by_type_src(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
gtype alias for $1;
src alias for $2;
is_an alias for $3;
query TEXT;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
query := ''SELECT DISTINCT f.feature_id
FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl
ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id)
WHERE t.name = '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src)
|| '' AND f.is_analysis = '' || quote_literal(is_an) || '';'';
IF (STRPOS(gtype, ''%'') > 0) THEN
query := ''SELECT DISTINCT f.feature_id
FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id) INNER join featureloc fl
ON (f.feature_id = fl.feature_id) INNER join feature src ON (src.feature_id = fl.srcfeature_id)
WHERE t.name like '' || quote_literal(gtype) || '' AND src.uniquename = '' || quote_literal(src)
|| '' AND f.is_analysis = '' || quote_literal(is_an) || '';'';
END IF;
FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
RETURN NEXT myrc;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
CREATE OR REPLACE FUNCTION get_feature_ids_by_type_name(cvterm.name%TYPE, feature.uniquename%TYPE, char(1)) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
gtype alias for $1;
name alias for $2;
is_an alias for $3;
query TEXT;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
query := ''SELECT DISTINCT f.feature_id
FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id)
WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename = '' || quote_literal(name)
|| '' OR f.name = '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';'';
IF (STRPOS(name, ''%'') > 0) THEN
query := ''SELECT DISTINCT f.feature_id
FROM feature f INNER join cvterm t ON (f.type_id = t.cvterm_id)
WHERE t.name = '' || quote_literal(gtype) || '' AND (f.uniquename like '' || quote_literal(name)
|| '' OR f.name like '' || quote_literal(name) || '') AND f.is_analysis = '' || quote_literal(is_an) || '';'';
END IF;
FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
RETURN NEXT myrc;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
--- get all feature ids (including children) for feature that has an ontology term (say GO function)
CREATE OR REPLACE FUNCTION get_feature_ids_by_ont(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
aspect alias for $1;
term alias for $2;
query TEXT;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
query := ''SELECT DISTINCT fcvt.feature_id
FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND
t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) ||
'' AND t.name = '' || quote_literal(term) || '';'';
IF (STRPOS(term, ''%'') > 0) THEN
query := ''SELECT DISTINCT fcvt.feature_id
FROM feature_cvterm fcvt, cv, cvterm t WHERE cv.cv_id = t.cv_id AND
t.cvterm_id = fcvt.cvterm_id AND cv.name = '' || quote_literal(aspect) ||
'' AND t.name like '' || quote_literal(term) || '';'';
END IF;
FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
RETURN NEXT myrc;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
CREATE OR REPLACE FUNCTION get_feature_ids_by_ont_root(cv.name%TYPE,cvterm.name%TYPE) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
aspect alias for $1;
term alias for $2;
query TEXT;
subquery TEXT;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id
AND cv.name = '' || quote_literal(aspect) || '' AND t.name = '' || quote_literal(term) || '';'';
IF (STRPOS(term, ''%'') > 0) THEN
subquery := ''SELECT t.cvterm_id FROM cv, cvterm t WHERE cv.cv_id = t.cv_id
AND cv.name = '' || quote_literal(aspect) || '' AND t.name like '' || quote_literal(term) || '';'';
END IF;
query := ''SELECT DISTINCT fcvt.feature_id
FROM feature_cvterm fcvt INNER JOIN (SELECT cvterm_id FROM get_it_sub_cvterm_ids('' || quote_literal(subquery) || '')) AS ont ON (fcvt.cvterm_id = ont.cvterm_id);'';
FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
RETURN NEXT myrc;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
--- get all feature ids (including children) for feature with the property (type, val)
CREATE OR REPLACE FUNCTION get_feature_ids_by_property(cvterm.name%TYPE,varchar) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
p_type alias for $1;
p_val alias for $2;
query TEXT;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
query := ''SELECT DISTINCT fprop.feature_id
FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' ||
quote_literal(p_type) || '' AND fprop.value = '' || quote_literal(p_val) || '';'';
IF (STRPOS(p_val, ''%'') > 0) THEN
query := ''SELECT DISTINCT fprop.feature_id
FROM featureprop fprop, cvterm t WHERE t.cvterm_id = fprop.type_id AND t.name = '' ||
quote_literal(p_type) || '' AND fprop.value like '' || quote_literal(p_val) || '';'';
END IF;
FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
RETURN NEXT myrc;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
--- get all feature ids (including children) for feature with the property val
CREATE OR REPLACE FUNCTION get_feature_ids_by_propval(varchar) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
p_val alias for $1;
query TEXT;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type%ROWTYPE;
BEGIN
query := ''SELECT DISTINCT fprop.feature_id
FROM featureprop fprop WHERE fprop.value = '' || quote_literal(p_val) || '';'';
IF (STRPOS(p_val, ''%'') > 0) THEN
query := ''SELECT DISTINCT fprop.feature_id
FROM featureprop fprop WHERE fprop.value like '' || quote_literal(p_val) || '';'';
END IF;
FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
RETURN NEXT myrc;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
---4 args: ptype, ctype, count, operator (valid SQL number comparison operator), and is_analysis
---get feature ids for any node with type = ptype whose child node type = ctype
---and child node feature count comparing (using operator) to ccount
CREATE OR REPLACE FUNCTION get_feature_ids_by_child_count(cvterm.name%TYPE, cvterm.name%TYPE, INTEGER, varchar, char(1)) RETURNS SETOF feature_by_fx_type AS
'
DECLARE
ptype alias for $1;
ctype alias for $2;
ccount alias for $3;
operator alias for $4;
is_an alias for $5;
query TEXT;
myrc feature_by_fx_type%ROWTYPE;
myrc2 feature_by_fx_type %ROWTYPE;
BEGIN
query := ''SELECT DISTINCT f.feature_id
FROM feature f INNER join (select count(*) as c, p.feature_id FROM feature p
INNER join cvterm pt ON (p.type_id = pt.cvterm_id) INNER join feature_relationship fr
ON (p.feature_id = fr.object_id) INNER join feature c ON (c.feature_id = fr.subject_id)
INNER join cvterm ct ON (c.type_id = ct.cvterm_id)
WHERE pt.name = '' || quote_literal(ptype) || '' AND ct.name = '' || quote_literal(ctype)
|| '' AND p.is_analysis = '' || quote_literal(is_an) || '' group by p.feature_id) as cq
ON (cq.feature_id = f.feature_id) WHERE cq.c '' || operator || ccount || '';'';
---RAISE NOTICE ''%'', query;
FOR myrc IN SELECT * FROM get_feature_ids(query) LOOP
RETURN NEXT myrc;
END LOOP;
RETURN;
END;
'
LANGUAGE 'plpgsql';
|
