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# pylint: disable-all
import collections
from flask import g
from dataclasses import dataclass
class TheSpecies:
def __init__(self, dataset=None, species_name=None):
if species_name is not None:
self.name = species_name
self.chromosomes = Chromosomes(species=self.name)
else:
self.dataset = dataset
self.chromosomes = Chromosomes(dataset=self.dataset)
class Chromosomes:
def __init__(self, dataset=None, species=None):
self.chromosomes = collections.OrderedDict()
if species is not 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)
# @dataclass
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
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