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Diffstat (limited to 'wqflask/base/species.py')
| -rw-r--r-- | wqflask/base/species.py | 117 |
1 files changed, 117 insertions, 0 deletions
diff --git a/wqflask/base/species.py b/wqflask/base/species.py new file mode 100644 index 00000000..9d4cac4c --- /dev/null +++ b/wqflask/base/species.py @@ -0,0 +1,117 @@ +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 + +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, length): + 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() + + 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 + """, self.dataset.group.name).fetchall() + print("bike:", results) + + for item in results: + self.chromosomes[item.Name] = IndChromosome(item.Length) + + self.set_mb_graph_interval() + self.get_cm_length_list() + + + def set_mb_graph_interval(self): + """Empirical megabase interval""" + + #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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