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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
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