Datasets:
Formats:
parquet
Languages:
English
Size:
10M - 100M
Tags:
biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
License:
File size: 5,269 Bytes
6d1bbc7 | 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 | """Database connection and migration runner for NegBioDB GE (Gene Essentiality) domain.
Reuses the Common Layer from negbiodb.db (get_connection, connect,
run_migrations) with GE-specific defaults.
"""
import glob
import os
from pathlib import Path
# Reuse Common Layer infrastructure
from negbiodb.db import get_connection, connect, get_applied_versions # noqa: F401
_PROJECT_ROOT = Path(__file__).resolve().parent.parent.parent
DEFAULT_GE_DB_PATH = _PROJECT_ROOT / "data" / "negbiodb_depmap.db"
DEFAULT_GE_MIGRATIONS_DIR = _PROJECT_ROOT / "migrations_depmap"
def run_ge_migrations(
db_path: str | Path | None = None,
migrations_dir: str | Path | None = None,
) -> list[str]:
"""Apply pending GE-domain migrations to the database.
Mirrors negbiodb.db.run_migrations but uses GE-specific defaults.
"""
if db_path is None:
db_path = DEFAULT_GE_DB_PATH
if migrations_dir is None:
migrations_dir = DEFAULT_GE_MIGRATIONS_DIR
db_path = Path(db_path)
migrations_dir = Path(migrations_dir)
db_path.parent.mkdir(parents=True, exist_ok=True)
conn = get_connection(db_path)
try:
applied = get_applied_versions(conn)
migration_files = sorted(glob.glob(str(migrations_dir / "*.sql")))
newly_applied = []
for mf in migration_files:
version = os.path.basename(mf).split("_")[0]
if version not in applied:
with open(mf) as f:
sql = f.read()
conn.executescript(sql)
newly_applied.append(version)
return newly_applied
finally:
conn.close()
def create_ge_database(
db_path: str | Path | None = None,
migrations_dir: str | Path | None = None,
) -> Path:
"""Create a new GE database by running all GE migrations."""
if db_path is None:
db_path = DEFAULT_GE_DB_PATH
db_path = Path(db_path)
applied = run_ge_migrations(db_path, migrations_dir)
if applied:
print(f"Applied {len(applied)} GE migration(s): {', '.join(applied)}")
else:
print("GE database is up to date (no pending migrations).")
return db_path
def refresh_all_ge_pairs(conn) -> int:
"""Refresh gene_cell_pairs aggregation from ge_negative_results.
Deletes all existing pairs and re-aggregates, computing best confidence,
best evidence type, score ranges, and degree counts.
"""
conn.execute("DELETE FROM ge_split_assignments")
conn.execute("DELETE FROM gene_cell_pairs")
conn.execute(
"""INSERT INTO gene_cell_pairs
(gene_id, cell_line_id, num_screens, num_sources,
best_confidence, best_evidence_type,
min_gene_effect, max_gene_effect, mean_gene_effect)
SELECT
gene_id,
cell_line_id,
COUNT(DISTINCT COALESCE(screen_id, -1)),
COUNT(DISTINCT source_db),
CASE MIN(CASE confidence_tier
WHEN 'gold' THEN 1 WHEN 'silver' THEN 2
WHEN 'bronze' THEN 3 END)
WHEN 1 THEN 'gold' WHEN 2 THEN 'silver'
WHEN 3 THEN 'bronze' END,
CASE MIN(CASE evidence_type
WHEN 'reference_nonessential' THEN 1
WHEN 'multi_screen_concordant' THEN 2
WHEN 'crispr_nonessential' THEN 3
WHEN 'rnai_nonessential' THEN 4
WHEN 'context_nonessential' THEN 5 END)
WHEN 1 THEN 'reference_nonessential'
WHEN 2 THEN 'multi_screen_concordant'
WHEN 3 THEN 'crispr_nonessential'
WHEN 4 THEN 'rnai_nonessential'
WHEN 5 THEN 'context_nonessential' END,
MIN(gene_effect_score),
MAX(gene_effect_score),
AVG(gene_effect_score)
FROM ge_negative_results
GROUP BY gene_id, cell_line_id"""
)
# Compute gene_degree: number of cell lines where this gene is non-essential
conn.execute("DROP TABLE IF EXISTS _gdeg")
conn.execute(
"""CREATE TEMP TABLE _gdeg (
gene_id INTEGER PRIMARY KEY, deg INTEGER)"""
)
conn.execute(
"""INSERT INTO _gdeg
SELECT gene_id, COUNT(DISTINCT cell_line_id)
FROM gene_cell_pairs GROUP BY gene_id"""
)
conn.execute(
"""UPDATE gene_cell_pairs SET gene_degree = (
SELECT deg FROM _gdeg d
WHERE d.gene_id = gene_cell_pairs.gene_id
)"""
)
conn.execute("DROP TABLE _gdeg")
# Compute cell_line_degree: number of genes non-essential in this cell line
conn.execute("DROP TABLE IF EXISTS _cldeg")
conn.execute(
"""CREATE TEMP TABLE _cldeg (
cell_line_id INTEGER PRIMARY KEY, deg INTEGER)"""
)
conn.execute(
"""INSERT INTO _cldeg
SELECT cell_line_id, COUNT(DISTINCT gene_id)
FROM gene_cell_pairs GROUP BY cell_line_id"""
)
conn.execute(
"""UPDATE gene_cell_pairs SET cell_line_degree = (
SELECT deg FROM _cldeg d
WHERE d.cell_line_id = gene_cell_pairs.cell_line_id
)"""
)
conn.execute("DROP TABLE _cldeg")
count = conn.execute(
"SELECT COUNT(*) FROM gene_cell_pairs"
).fetchone()[0]
return count
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