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from collections import OrderedDict
from dataclasses import dataclass
from dataclasses import InitVar
from typing import Optional, Dict, Any, Union
from wqflask.database import database_connection
@dataclass
class TheSpecies:
"""Data related to species."""
dataset: Optional[Dict] = None
species_name: Optional[str] = None
def __post_init__(self) -> None:
# Just an alias of species_name. It's safe for this to be None.
self.name = self.species_name
with database_connection() as conn:
self.chromosomes = Chromosomes(conn=conn,
species=self.species_name,
dataset=self.dataset)
@dataclass
class IndChromosome:
"""Data related to IndChromosome"""
name: str
length: int
@property
def mb_length(self) -> Union[int, float]:
"""Chromosome length in mega-bases"""
return self.length / 1000000
@dataclass
class Chromosomes:
"""Data related to a chromosome"""
conn: Any
dataset: InitVar[Dict] = None
species: Optional[str] = None
def __post_init__(self, dataset) -> None:
if self.species is None:
self.dataset = dataset
@property
def chromosomes(self) -> OrderedDict:
"""Lazily fetch the chromosomes"""
chromosomes = OrderedDict()
with self.conn.cursor() as cursor:
if self.species is not None:
cursor.execute(
"SELECT Chr_Length.Name, Chr_Length.OrderId, Length "
"FROM Chr_Length, Species WHERE "
"Chr_Length.SpeciesId = Species.SpeciesId AND "
"Species.Name = %s "
"ORDER BY OrderId", (self.species.capitalize(),))
else:
cursor.execute(
"SELECT Chr_Length.Name, Chr_Length.OrderId, "
"Length FROM Chr_Length, InbredSet WHERE "
"Chr_Length.SpeciesId = InbredSet.SpeciesId AND "
"InbredSet.Name = "
"%s ORDER BY OrderId", (self.dataset.group.name,))
for name, _, length in cursor.fetchall():
chromosomes[name] = IndChromosome(
name=name, length=length)
return chromosomes
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