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authorZachary Sloan2013-01-03 18:15:32 -0600
committerZachary Sloan2013-01-03 18:15:32 -0600
commit91ed29ef68e8ad29b728f7f574ccc83730d9f7ab (patch)
tree14ab5e3014f5c0a1d8197d2a5587b627e97133ea /wqflask/base/species.py
parentfb1c44d09f47fa2e72a90df286ff8bb2a3107f2c (diff)
downloadgenenetwork2-91ed29ef68e8ad29b728f7f574ccc83730d9f7ab.tar.gz
Began working on marker_regression.py and created Chromosomes class
in species.py
Diffstat (limited to 'wqflask/base/species.py')
-rw-r--r--wqflask/base/species.py52
1 files changed, 42 insertions, 10 deletions
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 98941ce5..1fd76772 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -1,16 +1,48 @@
-from __future__ import print_function, division
+from __future__ import absolute_import, print_function, division
+import collections
+
+from flask import Flask, g
+
+#from MySQLdb import escape_string as escape
+
+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.group.name)
+
+ #@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 Chromosomes(object):
+ def __init__(self, group_name):
+ 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
+ """, group_name).fetchall()
+ print("bike:", results)
+
+ for item in results:
+ self.chromosomes[item.Name] = item.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))
-
- return chromosomes
+ print("self.chromosomes:", self.chromosomes)