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from dataclasses import dataclass
from typing import Optional, Union
from collections import OrderedDict
class TheSpecies:
"""Data related to species."""
def __init__(self, dataset=None, species_name=None) -> None:
"Initialise the Species object"
self.dataset = dataset
self.name = self.species_name = species_name
self.chromosomes = Chromosomes(species=species_name,
dataset=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"""
def __init__(self, dataset, species: Optional[str]) -> None:
"initialise the Chromosome object"
self.species = species
if species is None:
self.dataset = dataset
def chromosomes(self, db_cursor) -> OrderedDict:
"""Lazily fetch the chromosomes"""
chromosomes = OrderedDict()
if self.species is not None:
db_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:
db_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 db_cursor.fetchall():
chromosomes[name] = IndChromosome(
name=name, length=length)
return chromosomes
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