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-rwxr-xr-xwqflask/base/data_set.py34
1 files changed, 19 insertions, 15 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index beb62bd7..f25e7974 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -168,13 +168,13 @@ class Markers(object):
for marker, p_value in itertools.izip(self.markers, p_values):
marker['p_value'] = p_value
- if marker['p_value'] == 0:
- marker['lod_score'] = 0
- marker['lrs_value'] = 0
- else:
- marker['lod_score'] = -math.log10(marker['p_value'])
- #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
- marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
+ if math.isnan(marker['p_value']):
+ print("p_value is:", marker['p_value'])
+ marker['lod_score'] = -math.log10(marker['p_value'])
+ #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
+ marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
+
+
class HumanMarkers(Markers):
@@ -189,6 +189,8 @@ class HumanMarkers(Markers):
marker['name'] = splat[1]
marker['Mb'] = float(splat[3]) / 1000000
self.markers.append(marker)
+
+ #print("markers is: ", pf(self.markers))
def add_pvalues(self, p_values):
@@ -315,12 +317,12 @@ class DatasetGroup(object):
#determine default genotype object
if self.incparentsf1 and genotype_1.type != "intercross":
- genotype = genotype_2
+ self.genotype = genotype_2
else:
self.incparentsf1 = 0
- genotype = genotype_1
+ self.genotype = genotype_1
- self.samplelist = list(genotype.prgy)
+ self.samplelist = list(self.genotype.prgy)
#class DataSets(object):
@@ -438,10 +440,12 @@ class DataSet(object):
def get_trait_data(self, sample_list=None):
if sample_list:
- self.samplelist = sample_list + self.group.parlist + self.group.f1list
+ self.samplelist = sample_list
else:
- self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list
-
+ self.samplelist = self.group.samplelist
+
+ if (self.group.parlist + self.group.f1list) in self.samplelist:
+ self.samplelist += self.group.parlist + self.group.f1list
query = """
SELECT Strain.Name, Strain.Id FROM Strain, Species
@@ -501,8 +505,8 @@ class DataSet(object):
and {}Freeze.Name = '{}'
and {}.Id = {}XRef.{}Id
order by {}.Id
- """.format(*mescape(self.type, self.type, self.type, self.type,
- self.name, dataset_type, self.type, self.type, dataset_type))
+ """.format(*mescape(self.type, self.type, self.type, self.name,
+ dataset_type, self.type, dataset_type, dataset_type))
else:
query += """
WHERE {}XRef.{}FreezeId = {}Freeze.Id