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resolved TODO comments in db.py and library.py #92

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resolved TODO comments in db.py and library.py #92

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3 changes: 0 additions & 3 deletions src/guidescanpy/flask/blueprints/library.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,6 @@ def library(
frac_control: float = 0.0,
append5: bool = False,
):
# TODO: Why is this \r\n and not just \n?
genes = genes.splitlines()

library_info = get_library_info_by_gene(organism, genes, n_guides)
Expand All @@ -64,7 +63,6 @@ def library(
results = []
for i, genes in enumerate(genes_by_pool_index):
n_essential_genes = round(frac_essential * len(genes))
# TODO: randomize
essential_genes = get_essential_genes(organism, n_essential_genes)
essential_genes_library_info = get_library_info_by_gene(
organism, essential_genes, n_guides
Expand All @@ -73,7 +71,6 @@ def library(
n_control_guides = round(
frac_control * len(genes)
) # TODO: Clojure code does this, but it doesn't seem correct
# TODO: randomize
control_guides = get_control_guides(organism, n_control_guides)

for gene in genes:
Expand Down
14 changes: 9 additions & 5 deletions src/guidescanpy/flask/db.py
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Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,7 @@ def create_region_query(organism, region):
results = conn.execute(query, {"organism": organism, "entrez_id": region})
for row in results.mappings():
return_value = dict(row)
# TODO: sqlite backend seems to return boolean as int

return_value["sense"] = bool(return_value["sense"])
return return_value

Expand Down Expand Up @@ -132,17 +132,21 @@ def get_library_info_by_gene(organism, genes, n_guides=6):
def get_essential_genes(organism, n=1):
conn = get_connection()
query = text(
"SELECT gene_symbol FROM essential_genes WHERE organism = :organism LIMIT :n"
"SELECT gene_symbol FROM essential_genes WHERE organism = :organism ORDER BY RANDOM() LIMIT :n"
)
results = conn.execute(query, {"organism": organism, "n": n})
return [r[0] for r in results] # TODO: Ugly!

return_value = []
for row in results.mappings():
return_value.append(row["gene_symbol"])
return return_value


def get_control_guides(organism, n=1):
conn = get_connection()
# TODO: Order by?

query = text(
"SELECT * FROM libraries WHERE organism = :organism AND (grna_type='safe_targeting_control' OR grna_type='non_targeting_control') LIMIT :n"
"SELECT * FROM libraries WHERE organism = :organism AND (grna_type='safe_targeting_control' OR grna_type='non_targeting_control') ORDER BY RANDOM() LIMIT :n"
)
results = conn.execute(query, {"organism": organism, "n": n})
return [dict(row) for row in results.mappings()]
Expand Down
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