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"""module contains species and chromosomes classes"""
import collections
from flask import g
from gn3.utility.logger import getLogger
logger = getLogger(__name__)
# pylint: disable=too-few-public-methods
# intentionally disabled check for few public methods
class TheSpecies:
"""class for Species"""
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 IndChromosome:
"""class for 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:
"""class for 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)
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