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"""Functions for handling genotypes."""
from typing import Optional
import MySQLdb as mdb
from MySQLdb.cursors import DictCursor
from uploader.db_utils import debug_query
def genocode_by_population(
conn: mdb.Connection, population_id: int) -> tuple[dict, ...]:
"""Get the allele/genotype codes."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT * FROM GenoCode WHERE InbredSetId=%s",
(population_id,))
return tuple(dict(item) for item in cursor.fetchall())
def genotype_markers_count(conn: mdb.Connection, species_id: int) -> int:
"""Find the total count of the genotype markers for a species."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"SELECT COUNT(Name) AS markers_count FROM Geno WHERE SpeciesId=%s",
(species_id,))
return int(cursor.fetchone()["markers_count"])
def genotype_markers(
conn: mdb.Connection,
species_id: int,
offset: int = 0,
limit: Optional[int] = None
) -> tuple[dict, ...]:
"""Retrieve markers from the database."""
_query = "SELECT * FROM Geno WHERE SpeciesId=%s"
if bool(limit) and limit > 0:
_query = _query + f" LIMIT {limit} OFFSET {offset}"
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(_query, (species_id,))
debug_query(cursor)
return tuple(dict(row) for row in cursor.fetchall())
def genotype_dataset(
conn: mdb.Connection,
species_id: int,
population_id: int,
dataset_id: Optional[int] = None
) -> Optional[dict]:
"""Retrieve genotype datasets from the database.
Apparently, you should only ever have one genotype dataset for a population.
"""
_query = (
"SELECT gf.* FROM Species AS s INNER JOIN InbredSet AS iset "
"ON s.Id=iset.SpeciesId INNER JOIN GenoFreeze AS gf "
"ON iset.Id=gf.InbredSetId "
"WHERE s.Id=%s AND iset.Id=%s")
_params = (species_id, population_id)
if bool(dataset_id):
_query = _query + " AND gf.Id=%s"
_params = _params + (dataset_id,)
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(_query, _params)
debug_query(cursor)
result = cursor.fetchone()
if bool(result):
return dict(result)
return None
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