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import collections
from dataclasses import dataclass
from typing import Optional, Dict
from flask import g
from utility.logger import getLogger
logger = getLogger(__name__)
@dataclass
class TheSpecies:
"""Data related to species."""
dataset: Optional[Dict] = None
species_name: Optional[str] = None
def __post_init__(self):
if self.species_name is not None:
self.name = self.species_name
self.chromosomes = Chromosomes(species=self.name)
else:
self.dataset = self.dataset
self.chromosomes = Chromosomes(dataset=self.dataset)
class IndChromosome:
def __init__(self, name, length):
self.name = name
self.length = length
@property
def mb_length(self):
"""Chromosome length in megabases"""
return self.length / 1000000
class Chromosomes:
def __init__(self, dataset=None, species=None):
self.chromosomes = collections.OrderedDict()
if species != None:
query = (
"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" % species.capitalize()
)
else:
self.dataset = dataset
query = (
"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)
logger.sql(query)
results = g.db.execute(query).fetchall()
for item in results:
self.chromosomes[item.OrderId] = IndChromosome(
item.Name, item.Length)
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