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Updates QC stats, fixes orthology counts, adds phenocubes & phenocube report #628

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Updates QC stats, fixes orthology counts, adds phenocubes & phenocube report #628

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92 changes: 80 additions & 12 deletions scripts/generate_reports.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -152,28 +152,26 @@ copy (
ortholog_counts as (
select
non_human_taxon,
sum(ortholog_count) as ortholog_count
count(*) as ortholog_count
from (
select
object_taxon as non_human_taxon,
count(distinct object) as ortholog_count
object as ortholog,
object_taxon as non_human_taxon
from denormalized_edges
where subject_taxon = 'NCBITaxon:9606'
where subject_taxon = 'NCBITaxon:9606'
and subject_category = 'biolink:Gene'
and object_category = 'biolink:Gene'
and predicate = 'biolink:orthologous_to'
group by object_taxon
union all
select
subject_taxon as non_human_taxon,
count(distinct subject) as ortholog_count
union
select
subject as ortholog,
subject_taxon as non_human_taxon
from denormalized_edges
where subject_category = 'biolink:Gene'
and object_category = 'biolink:Gene'
and object_taxon = 'NCBITaxon:9606'
and object_taxon = 'NCBITaxon:9606'
and predicate = 'biolink:orthologous_to'
group by subject_taxon
) as combined_ortholog_counts
)
group by non_human_taxon
)
select
Expand All @@ -189,3 +187,73 @@ copy (
from ortholog_counts
) to 'output/qc/human_orthology_coverage.parquet';

create or replace temporary table phenotype_to_phenotype as (
select upheno_left.subject as phenotype_left, upheno_left.object as upheno_term, upheno_right.subject as phenotype_right
from denormalized_edges upheno_left, denormalized_edges upheno_right
where upheno_left.predicate = 'biolink:subclass_of'
and upheno_right.predicate = 'biolink:subclass_of'
and upheno_left.object_namespace = 'UPHENO'
and upheno_right.object_namespace = 'UPHENO'
and upheno_left.subject_namespace <> 'UPHENO'
and upheno_right.subject_namespace <> 'UPHENO'
and upheno_left.object = upheno_right.object
and upheno_left.subject <> upheno_right.subject
);

copy (
with human_orthology as (
select
subject as human_gene,
object as ortholog
from denormalized_edges
where subject_taxon = 'NCBITaxon:9606'
and subject_category = 'biolink:Gene'
and object_category = 'biolink:Gene'
and predicate = 'biolink:orthologous_to'
union all
select
object as human_gene,
subject as ortholog
from denormalized_edges
where subject_category = 'biolink:Gene'
and object_category = 'biolink:Gene'
and object_taxon = 'NCBITaxon:9606'
and predicate = 'biolink:orthologous_to'
),
human_g2p as (
select subject as gene, object as phenotype
from denormalized_edges
where subject_namespace = 'HGNC'
and object_namespace = 'HP'
and predicate = 'biolink:has_phenotype'
),
ortholog_g2p as (
select subject as gene, object as phenotype
from denormalized_edges
where predicate = 'biolink:has_phenotype'
and subject_namespace <> 'HGNC'
and object_namespace <> 'HP'
)
select
ortholog_g2p.phenotype as non_human_phenotype,
human_orthology.ortholog as non_human_gene,
human_g2p.gene as human_gene,
human_g2p.phenotype as human_phenotype
from human_orthology
join human_g2p on human_orthology.human_gene = human_g2p.gene
join ortholog_g2p on human_orthology.ortholog = ortholog_g2p.gene
join phenotype_to_phenotype
on human_g2p.phenotype = phenotype_to_phenotype.phenotype_left
and ortholog_g2p.phenotype = phenotype_to_phenotype.phenotype_right
) to 'output/qc/phenocubes.parquet';

copy (
select
split_part(human_gene, ':', 1) as human_gene,
split_part(human_phenotype, ':', 1) as human_phenotype,
split_part(non_human_phenotype, ':', 1) as non_human_phenotype,
split_part(non_human_gene, ':', 1) as non_human_gene,
count(*) as count
from 'output/qc/phenocubes.parquet' group by all
) to 'output/qc/phenocubes_report.parquet';