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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 utility import Bunch
from pprint import pformat as pf
from utility.logger import getLogger
logger = getLogger(__name__ )
class TheSpecies(object):
def __init__(self, dataset):
self.dataset = dataset
#print("self.dataset is:", pf(self.dataset.__dict__))
self.chromosomes = Chromosomes(self.dataset)
self.genome_mb_length = self.chromosomes.get_genome_mb_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 IndChromosome(object):
def __init__(self, name, length):
self.name = name
self.length = length
@property
def mb_length(self):
"""Chromosome length in megabases"""
return self.length / 1000000
def set_cm_length(self, genofile_chr):
self.cm_length = genofile_chr[-1].cM - genofile_chr[0].cM
class Chromosomes(object):
def __init__(self, dataset):
self.dataset = dataset
self.chromosomes = collections.OrderedDict()
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)
self.set_mb_graph_interval()
#self.get_cm_length_list()
def set_mb_graph_interval(self):
"""Empirical megabase interval"""
if self.chromosomes:
self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
else:
self.mb_graph_interval = 1
#if self.chromosomes:
#assert self.chromosomes, "Have to add some code back in apparently to set it to 1"
#self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
#else:
#self.mb_graph_interval = 1
def get_genome_mb_length(self):
"""Gets the sum of each chromosome's length in megabases"""
return sum([ind_chromosome.mb_length for ind_chromosome in self.chromosomes.values()])
def get_genome_cm_length(self):
"""Gets the sum of each chromosome's length in centimorgans"""
return sum([ind_chromosome.cm_length for ind_chromosome in self.chromosomes.values()])
def get_cm_length_list(self):
"""Chromosome length in centimorgans
Calculates the length in centimorgans by subtracting the centimorgan position
of the last marker in a chromosome by the position of the first marker
"""
self.dataset.group.read_genotype_file()
self.cm_length_list = []
for chromosome in self.dataset.group.genotype:
self.cm_length_list.append(chromosome[-1].cM - chromosome[0].cM)
print("self.cm_length_list:", pf(self.cm_length_list))
assert len(self.cm_length_list) == len(self.chromosomes), "Uh-oh lengths should be equal!"
for counter, chromosome in enumerate(self.chromosomes.values()):
chromosome.cm_length = self.cm_length_list[counter]
#self.chromosomes[counter].cm_length = item
for key, value in self.chromosomes.items():
print("bread - %s: %s" % (key, pf(vars(value))))
# Testing
#if __name__ == '__main__':
# foo = dict(bar=dict(length))
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