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"""Load genotypes from R/qtl2 bundle into the database."""
import sys
import uuid
import logging
import traceback
from pathlib import Path
from zipfile import ZipFile
from argparse import ArgumentParser
import MySQLdb as mdb
from redis import Redis
from MySQLdb.cursors import DictCursor
from r_qtl import r_qtl2 as rqtl2
from quality_control.parsing import take
from qc_app.db_utils import database_connection
from qc_app.check_connections import check_db, check_redis
from scripts.redis_logger import RedisLogger
stderr_handler = logging.StreamHandler(stream=sys.stderr)
logger = logging.getLogger("install_genotypes")
logger.addHandler(stderr_handler)
def insert_markers(dbconn: mdb.Connection,
speciesid: int,
markers: tuple[str, ...]) -> int:
"""Insert genotype and genotype values into the database."""
with dbconn.cursor() as cursor:
cursor.executemany(
"INSERT INTO Geno(SpeciesId, Name, Marker_Name) "
"VALUES (%(speciesid)s, %(marker)s, %(marker)s) "
"ON DUPLICATE KEY UPDATE SpeciesId=SpeciesId",
tuple({"speciesid": speciesid, "marker": marker}
for marker in markers))
return cursor.rowcount
def insert_individuals(dbconn: mdb.Connection,
speciesid: int,
individuals: tuple[str, ...]) -> int:
"""Insert individuals/samples into the database."""
with dbconn.cursor() as cursor:
cursor.executemany(
"INSERT INTO Strain(Name, Name2, SpeciesId) "
"VALUES(%(id)s, %(id)s, %(speciesid)s) "
"ON DUPLICATE KEY UPDATE Name=Name",
tuple({"speciesid": speciesid, "id": individual}
for individual in individuals))
return cursor.rowcount
def cross_reference_individuals(dbconn: mdb.Connection,
speciesid: int,
populationid: int,
individuals: tuple[str, ...]) -> int:
"""Cross reference any inserted individuals."""
with dbconn.cursor(cursorclass=DictCursor) as cursor:
paramstr = ", ".join(["%s"] * len(individuals))
cursor.execute(f"SELECT Id FROM Strain WHERE Name IN ({paramstr})",
individuals)
ids = ({"popid": populationid, "indid": row["Id"]}
for row in cursor.fetchall())
cursor.executemany(
"INSERT INTO StrainXRef(InbredSetId, StrainId) "
"VALUES(%(popid)s, %(indid)s) "
"ON DUPLICATE KEY UPDATE InbredSetId=InbredSetId",
tuple(ids))
return cursor.rowcount
def insert_genotype_data(dbconn: mdb.Connection,
speciesid: int,
genotypes: tuple[dict, ...],
individuals: tuple[str, ...]) -> tuple[int, tuple[int, ...]]:
"""Insert the genotype data values into the database."""
with dbconn.cursor(cursorclass=DictCursor) as cursor:
paramstr = ", ".join(["%s"] * len(individuals))
cursor.execute(
f"SELECT Id, Name FROM Strain WHERE Name IN ({paramstr})",
individuals)
indids = {row["Name"]: row["Id"] for row in cursor.fetchall()}
markers = tuple(key for key in genotypes[0].keys() if key != "id")
paramstr = ", ".join(["%s"] * len(markers))
cursor.execute(
f"SELECT Id, Name FROM Geno WHERE SpeciesId=%s AND Name IN ({paramstr})",
(speciesid,)+markers)
markerids = {row["Name"]: row["Id"] for row in cursor.fetchall()}
cursor.execute("SELECT MAX(Id) AS lastid FROM GenoData")
lastid = cursor.fetchone()["lastid"]
data = tuple(
{**row, "gid": gid}
for gid, row in enumerate(
({
"value": innerrow[marker],
"indid": indids[innerrow["id"]],
"markerid": markerids[marker]
} for innerrow in genotypes for marker in
(key for key in innerrow.keys() if key != "id")),
start=lastid+1))
cursor.executemany(
"INSERT INTO GenoData(Id, StrainId, value) "
"VALUES(%(gid)s, %(indid)s, %(value)s)",
data)
return cursor.rowcount, tuple({
"dataid": row["gid"],
"markerid": row["markerid"]
} for row in data)
def cross_reference_genotypes(dbconn: mdb.Connection,
datasetid: int,
dataids: tuple[int, ...]) -> int:
"""Cross-reference the data to the relevant dataset."""
with dbconn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"INSERT INTO GenoXRef(GenoFreezeId, GenoId, DataId) "
"VALUES(%(datasetid)s, %(markerid)s, %(dataid)s) "
"ON DUPLICATE KEY UPDATE GenoFreezeId=GenoFreezeId",
tuple({**row, "datasetid": datasetid} for row in dataids))
return cursor.rowcount
def install_genotypes(dbconn: mdb.Connection,
speciesid: int,
populationid: int,
rqtl2bundle: Path) -> int:
"""Load any existing genotypes into the database."""
count = 0
with ZipFile(str(rqtl2bundle.absolute()), "r") as zfile:
try:
logger.info("Validating bundle")
rqtl2.validate_bundle(zfile)
logger.info("Bundle validated successfully.")
logger.info(("Loading genotypes. This could take a while. "
"Please be patient."))
cdata = rqtl2.control_data(zfile)
genotypes = rqtl2.file_data(zfile,
"geno",
cdata,
rqtl2.make_process_data_geno(cdata))
while True:
batch = tuple(take(genotypes, 5000))
if len(batch) == 0:
logger.info("Loading Genotypes complete!")
logger.info(
"Total rows processed: %s", count)
break
insert_markers(
dbconn,
speciesid,
tuple(key for key in batch[0].keys() if key != "id"))
individuals = tuple(row["id"] for row in batch)
insert_individuals(dbconn, speciesid, individuals)
cross_reference_individuals(
dbconn, speciesid, populationid, individuals)
_num_rows, dataids = insert_genotype_data(
dbconn, speciesid, batch, individuals)
cross_reference_genotypes(dbconn, datasetid, dataids)
count = count + len(batch)
if "gmap" in cdata:
logger.info("Loading genetic mapping info.")
# TODO: load gmap files
logger.info("Successfully loaded genetic mapping.")
if "pmap" in cdata:
logger.info("Loading physical mapping info.")
# TODO: load pmap files
logger.info("Successfully loaded physical mapping.")
except rqtl2.InvalidFormat as exc:
logger.error(str(exc))
logger.info("There are no genotypes to load.")
except Exception as _exc:
logger.error("Failing with exception: %s", traceback.format_exc())
return 3
return 0
if __name__ == "__main__":
def cli_args():
"""Process command-line arguments for install_genotypes"""
parser = ArgumentParser(
prog="install_genotypes",
description="Parse genotypes from R/qtl2 bundle into the database.")
parser.add_argument("databaseuri", help="URL to MariaDB")
parser.add_argument("redisuri", help="URL to Redis")
parser.add_argument("jobid",
help="Job ID that this belongs to.",
type=uuid.UUID)
parser.add_argument("speciesid",
help="Species to which bundle relates.")
parser.add_argument("populationid",
help="Population to group data under")
parser.add_argument("rqtl2bundle",
help="Path to R/qtl2 bundle zip file.",
type=Path)
parser.add_argument("--redisexpiry",
help="How long to keep any redis keys around.",
type=int,
default=86400)
return parser.parse_args()
def main():
"""Run `install_genotypes` scripts."""
args = cli_args()
check_db(args.databaseuri)
check_redis(args.redisuri)
if not args.rqtl2bundle.exists():
logging.error("File not found: '%s'.", args.rqtl2bundle)
return 2
with (Redis.from_url(args.redisuri, decode_responses=True) as rconn,
database_connection(args.databaseuri) as dbconn):
formatter = logging.Formatter(
"%(asctime)s - %(name)s - %(levelname)s: %(message)s")
job_messagelist = f"{str(args.jobid)}:log-messages"
rconn.hset(name=str(args.jobid),
key="log-messagelist",
value=job_messagelist)
redislogger = RedisLogger(
rconn, args.jobid, expiry=args.redisexpiry)
redislogger.setFormatter(formatter)
logger.addHandler(redislogger)
logger.setLevel("INFO")
return install_genotypes(dbconn,
args.speciesid,
args.populationid,
args.rqtl2bundle)
sys.exit(main())
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