diff options
Diffstat (limited to 'wqflask/base/species.py')
| -rw-r--r-- | wqflask/base/species.py | 27 |
1 files changed, 20 insertions, 7 deletions
diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 4ac2213c..6d99af65 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -14,10 +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) + 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): @@ -30,11 +33,21 @@ class IndChromosome(object): return self.length / 1000000 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 |