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authorZachary Sloan2013-03-12 22:22:49 +0000
committerZachary Sloan2013-03-12 22:22:49 +0000
commite71ec85ba3fc7ac45d035c7c1363b36aed709433 (patch)
tree7d64d2b2d5cedf0db0150076c6f0e2b5fdd31496 /wqflask/base
parent990d72e48c9fbf3fa976e435ad7645cfb8f3301d (diff)
downloadgenenetwork2-e71ec85ba3fc7ac45d035c7c1363b36aed709433.tar.gz
Got cashing working with pickle
Diffstat (limited to 'wqflask/base')
-rwxr-xr-xwqflask/base/data_set.py45
-rw-r--r--wqflask/base/species.py2
2 files changed, 24 insertions, 23 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index d474302c..10f047f8 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -95,11 +95,14 @@ class DatasetGroup(object):
if self.name == 'BXD300':
self.name = "BXD"
+ self.f1list = None
+ self.parlist = None
+ self.get_f1_parent_strains()
+ print("parents/f1s: {}:{}".format(self.parlist, self.f1list))
+
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
self.incparentsf1 = False
- self.f1list = None
- self.parlist = None
self.allsamples = None
self.markers = Markers(self.name)
@@ -117,6 +120,18 @@ class DatasetGroup(object):
# markers = json.load(json_data)
#
+ def get_f1_parent_strains(self):
+ try:
+ # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
+ f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
+ except KeyError:
+ f1 = f12 = maternal = paternal = None
+
+ if f1 and f12:
+ self.f1list = [f1, f12]
+ if maternal and paternal:
+ self.parlist = [maternal, paternal]
+
def read_genotype_file(self):
'''Read genotype from .geno file instead of database'''
#if self.group == 'BXD300':
@@ -128,38 +143,24 @@ class DatasetGroup(object):
#genotype_2 is Dataset Object with parents and f1 (not for intercross)
genotype_1 = reaper.Dataset()
-
+
# reaper barfs on unicode filenames, so here we ensure it's a string
full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno'))
genotype_1.read(full_filename)
- print("Got to after read")
-
- try:
- # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
- f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
- except KeyError:
- f1 = f12 = maternal = paternal = None
-
-
- if genotype_1.type == "group" and maternal and paternal:
- genotype_2 = genotype_1.add(Mat=maternal, Pat=paternal) #, F1=_f1)
+ if genotype_1.type == "group" and self.parlist:
+ genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1)
else:
genotype_2 = genotype_1
#determine default genotype object
if self.incparentsf1 and genotype_1.type != "intercross":
- self.genotype = genotype_2
+ genotype = genotype_2
else:
self.incparentsf1 = 0
- self.genotype = genotype_1
-
- self.samplelist = list(self.genotype.prgy)
+ genotype = genotype_1
- if f1 and f12:
- self.f1list = [f1, f12]
- if maternal and paternal:
- self.parlist = [maternal, paternal]
+ self.samplelist = list(genotype.prgy)
class DataSet(object):
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 9d4cac4c..689e5c05 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -62,7 +62,7 @@ class Chromosomes(object):
self.chromosomes[item.Name] = IndChromosome(item.Length)
self.set_mb_graph_interval()
- self.get_cm_length_list()
+ #self.get_cm_length_list()
def set_mb_graph_interval(self):