from __future__ import absolute_import, print_function, division import collections from flask import Flask, g #from MySQLdb import escape_string as escape from pprint import pformat as pf class TheSpecies(object): def __init__(self, dataset): self.dataset = dataset print("self.dataset is:", pf(self.dataset.__dict__)) self.chromosomes = Chromosomes(self.dataset.group.name) self.genome_length = self.chromosomes.get_genome_length() #@property #def chromosomes(self): # chromosomes = [("All", -1)] # # for counter, genotype in enumerate(self.dataset.group.genotype): # if len(genotype) > 1: # chromosomes.append((genotype.name, counter)) # # print("chromosomes is: ", pf(chromosomes)) # # return chromosomes class Chromosomes(object): def __init__(self, group_name): self.chromosomes = collections.OrderedDict() results = g.db.execute(""" Select Chr_Length.Name, Length from Chr_Length, InbredSet where Chr_Length.SpeciesId = InbredSet.SpeciesId AND InbredSet.Name = %s Order by OrderId """, group_name).fetchall() print("bike:", results) for item in results: self.chromosomes[item.Name] = item.Length print("self.chromosomes:", self.chromosomes) def get_mb_length(self): """Gets the chromosome length in megabases""" mb_lengths = chr_length/1000000.0 for name, chr_length in self.chromosomes return mb_lengths def get_genome_length(self): """Gets the sum of each chromosome's length""" genome_length = 0 for name, value in self.chromosomes.items(): genome_length += value return genome_length