import collections from flask import Flask, g from utility.logger import getLogger logger = getLogger(__name__) class TheSpecies: def __init__(self, dataset=None, species_name=None): if species_name != None: self.name = species_name self.chromosomes = Chromosomes(species=self.name) else: self.dataset = 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)