aboutsummaryrefslogtreecommitdiff
path: root/wqflask/base/species.py
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask/base/species.py')
-rw-r--r--wqflask/base/species.py27
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