diff options
Diffstat (limited to 'wqflask/base/species.py')
| -rw-r--r-- | wqflask/base/species.py | 107 |
1 files changed, 21 insertions, 86 deletions
diff --git a/wqflask/base/species.py b/wqflask/base/species.py index ce763fc3..6d99af65 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -14,23 +14,13 @@ 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 + 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(object): def __init__(self, name, length): @@ -42,17 +32,22 @@ class IndChromosome(object): """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 + 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 = """ + query = """ Select Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet where @@ -64,64 +59,4 @@ class Chromosomes(object): 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)) + self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length)
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