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Copy pathSQL-SRA-QRY-anno-proportions.txt
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SQL-SRA-QRY-anno-proportions.txt
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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
union all
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%"
)
group by id
)
) group by score;