-
Notifications
You must be signed in to change notification settings - Fork 1
/
SQL-SRA-QRY-anno-distribution.txt
285 lines (254 loc) · 10.2 KB
/
SQL-SRA-QRY-anno-distribution.txt
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
create table study_exp_count as
select
stu.study_accession as stu_id, count(*) as total from study as stu
join
experiment as exp
on exp.study_accession = stu.study_accession
group by stu_id;
create table study_anno_distrib as
select
stu.study_accession id, exp_count.total as total, count(library_construction_protocol) as c from study as stu
join
experiment as exp
on exp.study_accession = stu.study_accession
join
study_exp_count as exp_count
on exp_count.stu_id = stu.study_accession
where
(
library_construction_protocol like "% shear%"
or library_construction_protocol like "% restriction%"
or library_construction_protocol like "% digest%"
or library_construction_protocol like "% fragment%"
or library_construction_protocol like "% breaks %"
or library_construction_protocol like "% nebulis%"
or library_construction_protocol like "% nebuliz%"
or library_construction_protocol like "% acoustic%"
or library_construction_protocol like "% sonic%"
) and
(
library_construction_protocol like "% adapter%"
or library_construction_protocol like "% ligat%"
or library_construction_protocol like "% blunt%"
or library_construction_protocol like "% phosphorylat%"
or library_construction_protocol like "% overhang"
or library_construction_protocol like "% t4-PNK%"
or library_construction_protocol like "% t4%"
or library_construction_protocol like "% pnk%"
or library_construction_protocol like "% kinase%"
or library_construction_protocol like "% a-tail%"
) and
(
library_construction_protocol like "% clone%"
or library_construction_protocol like "% clonin%"
or library_construction_protocol like "% pcr %"
or library_construction_protocol like "% amplif%"
or library_construction_protocol like "% polymerase%"
or library_construction_protocol like "% taq%"
or library_construction_protocol like "% phusion%"
or library_construction_protocol like "% temperat%"
or library_construction_protocol like "% thermal%"
or library_construction_protocol like "% anneal%"
or library_construction_protocol like "% denature%"
)
group by id
order by total, c;
-- Table of experiment record count for each study and frequency of this experiment record count
create table study_exp_distrib as
select total, count(*) as freq from study_exp_count group by total;
-- First we need a look-up table containing
-- All studies and corresponding total experiment record counts for that study
-- Next we create an intermediate results table containing the annotation type
-- the study and the proportion of experiment records annotated for the study
-- which is then grouped by the number of studies that have experiment records
-- that are annotated to that % level
-- NB: KLUDGE - Do this as two separate queries as SQLite doesn't like the single
-- unioned query it breaks for some reason even though the queries are the same
-- and have matching column results.
--
-- First execute one unioned query for frag, ligation, enrichment
-- insert the results into new table (anno_distrib), then perform another query
-- for all annotations and insert the results into anno_distrib.
create table anno_distrib as
select 'fragmentation' as anno, *, count(score) as score_c from
(
select id, total, c, cast (c as real)/cast (total as real) * 100 as score from
(
select
stu.study_accession id, exp_count.total as total, count(library_construction_protocol) as c from study as stu
join
experiment as exp
on exp.study_accession = stu.study_accession
join
study_exp_count as exp_count
on exp_count.stu_id = stu.study_accession
where
library_construction_protocol like "% shear%"
or library_construction_protocol like "% restriction%"
or library_construction_protocol like "% digest%"
or library_construction_protocol like "% fragment%"
or library_construction_protocol like "% breaks %"
or library_construction_protocol like "% nebulis%" or library_construction_protocol like "% nebuliz%"
or library_construction_protocol like "% acoustic%"
or library_construction_protocol like "% sonic%"
group by id
)
) group by score
union all
select 'ligation' as anno, *, count(score) as score_c from
(
select id, total, c, cast (c as real)/cast (total as real) * 100 as score from
(
select
stu.study_accession id, exp_count.total as total, count(library_construction_protocol) as c from study as stu
join
experiment as exp
on exp.study_accession = stu.study_accession
join
study_exp_count as exp_count
on exp_count.stu_id = stu.study_accession
where
library_construction_protocol like "% adapter%"
or library_construction_protocol like "% ligat%"
or library_construction_protocol like "% blunt%"
or library_construction_protocol like "% phosphorylat%"
or library_construction_protocol like "% overhang"
or library_construction_protocol like "% t4-PNK%"
or library_construction_protocol like "% t4%"
or library_construction_protocol like "% pnk%"
or library_construction_protocol like "% kinase%"
or library_construction_protocol like "% a-tail%"
group by id
)
) group by score
union all
select 'enrichment' as anno, *, count(score) as score_c from
(
select id, total, c, cast (c as real)/cast (total as real) * 100 as score from
(
select
stu.study_accession id, exp_count.total as total, count(library_construction_protocol) as c from study as stu
join
experiment as exp
on exp.study_accession = stu.study_accession
join
study_exp_count as exp_count
on exp_count.stu_id = stu.study_accession
where
library_construction_protocol like "% clone%"
or library_construction_protocol like "% clonin%"
or library_construction_protocol like "% pcr %"
or library_construction_protocol like "% amplif%"
or library_construction_protocol like "% polymerase%"
or library_construction_protocol like "% taq%"
or library_construction_protocol like "% phusion%"
or library_construction_protocol like "% temperat%"
or library_construction_protocol like "% thermal%"
or library_construction_protocol like "% anneal%"
or library_construction_protocol like "% denature%"
group by id
)
) group by score;
-- This is the remainder part of the results for the above unioned query
insert into anno_distrib
select 'all' as anno, *, count(score) as score_c from
(
select id, total, c, cast (c as real)/cast (total as real) * 100 as score from
(
select
stu.study_accession id, exp_count.total as total, count(library_construction_protocol) as c from study as stu
join
experiment as exp
on exp.study_accession = stu.study_accession
join
study_exp_count as exp_count
on exp_count.stu_id = stu.study_accession
where
(
library_construction_protocol like "% shear%"
or library_construction_protocol like "% restriction%"
or library_construction_protocol like "% digest%"
or library_construction_protocol like "% fragment%"
or library_construction_protocol like "% breaks %"
or library_construction_protocol like "% nebulis%"
or library_construction_protocol like "% nebuliz%"
or library_construction_protocol like "% acoustic%"
or library_construction_protocol like "% sonic%"
) and
(
library_construction_protocol like "% adapter%"
or library_construction_protocol like "% ligat%"
or library_construction_protocol like "% blunt%"
or library_construction_protocol like "% phosphorylat%"
or library_construction_protocol like "% overhang"
or library_construction_protocol like "% t4-PNK%"
or library_construction_protocol like "% t4%"
or library_construction_protocol like "% pnk%"
or library_construction_protocol like "% kinase%"
or library_construction_protocol like "% a-tail%"
) and
(
library_construction_protocol like "% clone%"
or library_construction_protocol like "% clonin%"
or library_construction_protocol like "% pcr %"
or library_construction_protocol like "% amplif%"
or library_construction_protocol like "% polymerase%"
or library_construction_protocol like "% taq%"
or library_construction_protocol like "% phusion%"
or library_construction_protocol like "% temperat%"
or library_construction_protocol like "% thermal%"
or library_construction_protocol like "% anneal%"
or library_construction_protocol like "% denature%"
)
group by id
)
) group by score;
-- Final break-down of proportions of experiment records annotated
-- for a study and annotation type, but binned into percentages
select anno, '> 0% <= 25%', sum(score_c) from anno_distrib
where (score <= 25) and anno = 'fragmentation'
union all
select anno, '> 25% <= 50%', sum(score_c) from anno_distrib
where (score > 25 and score <= 50) and anno = 'fragmentation'
union all
select anno, '> 50% <= 75%', sum(score_c) from anno_distrib
where (score > 50 and score <= 75) and anno = 'fragmentation'
union all
select anno, '> 75% <= 100%', sum(score_c) from anno_distrib
where (score > 75 and score <= 100) and anno = 'fragmentation'
union all
select anno, '> 0% <= 25%', sum(score_c) from anno_distrib
where (score <= 25) and anno = 'ligation'
union all
select anno, '> 25% <= 50%', sum(score_c) from anno_distrib
where (score > 25 and score <= 50) and anno = 'ligation'
union all
select anno, '> 50% <= 75%', sum(score_c) from anno_distrib
where (score > 50 and score <= 75) and anno = 'ligation'
union all
select anno, '> 75% <= 100%', sum(score_c) from anno_distrib
where (score > 75 and score <= 100) and anno = 'ligation'
union all
select anno, '> 0% <= 25%', sum(score_c) from anno_distrib
where (score <= 25) and anno = 'enrichment'
union all
select anno, '> 25% <= 50%', sum(score_c) from anno_distrib
where (score > 25 and score <= 50) and anno = 'enrichment'
union all
select anno, '> 50% <= 75%', sum(score_c) from anno_distrib
where (score > 50 and score <= 75) and anno = 'enrichment'
union all
select anno, '> 75% <= 100%', sum(score_c) from anno_distrib
where (score > 75 and score <= 100) and anno = 'enrichment'
union all
select anno, '> 0% <= 25%', sum(score_c) from anno_distrib
where (score <= 25) and anno = 'all'
union all
select anno, '> 25% <= 50%', sum(score_c) from anno_distrib
where (score > 25 and score <= 50) and anno = 'all'
union all
select anno, '> 50% <= 75%', sum(score_c) from anno_distrib
where (score > 50 and score <= 75) and anno = 'all'
union all
select anno, '> 75% <= 100%', sum(score_c) from anno_distrib
where (score > 75 and score <= 100) and anno = 'all';