Reaper mapping results are now correct and account for samples with two names (like BXD65a)

R/qtl and PYLMM still not working with the change and bootstrap results are also still wrong, so need to fix those issues.

4 files changed, 9 insertions, 46 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 053b45fc..4953e728 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -711,7 +711,7 @@ class PhenotypeDataSet(DataSet):
     def retrieve_sample_data(self, trait):
         query = """
                     SELECT
-                            Strain.Name, PublishData.value, PublishSE.error, NStrain.count
+                            Strain.Name, PublishData.value, PublishSE.error, NStrain.count, Strain.Name2
                     FROM
                             (PublishData, Strain, PublishXRef, PublishFreeze)
                     left join PublishSE on
@@ -803,7 +803,7 @@ class GenotypeDataSet(DataSet):
     def retrieve_sample_data(self, trait):
         query = """
                     SELECT
-                            Strain.Name, GenoData.value, GenoSE.error, GenoData.Id
+                            Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Sample.Name2
                     FROM
                             (GenoData, GenoFreeze, Strain, Geno, GenoXRef)
                     left join GenoSE on
@@ -1031,7 +1031,7 @@ class MrnaAssayDataSet(DataSet):
     def retrieve_sample_data(self, trait):
         query = """
                     SELECT
-                            Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id
+                            Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id, Strain.Name2
                     FROM
                             (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
                     left join ProbeSetSE on
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index af22b5a1..05ee3d96 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -180,13 +180,15 @@ class GeneralTrait(object):
         samples = []
         vals = []
         the_vars = []
+        sample_aliases = []
         for sample_name, sample_data in self.data.items():
             if sample_data.value != None:
                 if not include_variance or sample_data.variance != None:
                     samples.append(sample_name)
                     vals.append(sample_data.value)
                     the_vars.append(sample_data.variance)
-        return  samples, vals, the_vars
+                    sample_aliases.append(sample_data.name2)
+        return  samples, vals, the_vars, sample_aliases
 
 
     #
@@ -230,7 +232,7 @@ class GeneralTrait(object):
 
         if results:
             for item in results:
-                name, value, variance, num_cases = item
+                name, value, variance, num_cases, name2 = item
                 if not samplelist or (samplelist and name in samplelist):
                     self.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
 
@@ -308,46 +310,6 @@ class GeneralTrait(object):
                 if isinstance(trait_info[i], basestring):
                     holder = unicode(trait_info[i], "utf8", "ignore")
                 setattr(self, field, holder)
-<<<<<<< HEAD
-
-            description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8')
-            target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
-
-            if len(description_string) > 1 and description_string != 'None':
-                description_display = description_string
-            else:
-                description_display = self.symbol
-
-            if (len(description_display) > 1 and description_display != 'N/A' and
-                    len(target_string) > 1 and target_string != 'None'):
-                description_display = description_display + '; ' + target_string.strip()
-
-            # Save it for the jinja2 template
-            self.description_display = description_display
-
-            #XZ: trait_location_value is used for sorting
-            trait_location_repr = 'N/A'
-            trait_location_value = 1000000
-
-            if self.chr and self.mb:
-                #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
-                #This is so we can convert the location to a number used for sorting
-                trait_location_value = convert_location_to_value(self.chr, self.mb)
-                #try:
-                #    trait_location_value = int(self.chr)*1000 + self.mb
-                #except ValueError:
-                #    if self.chr.upper() == 'X':
-                #        trait_location_value = 20*1000 + self.mb
-                #    else:
-                #        trait_location_value = (ord(str(self.chr).upper()[0])*1000 +
-                #                               self.mb)
-
-                #ZS: Put this in function currently called "convert_location_to_value"
-                self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb))
-                self.location_value = trait_location_value
-                
-=======
->>>>>>> e0c5c1aae3aaaa1d81bcec36835a97e169dcc2e2
                 
             if self.dataset.type == 'Publish':
                 self.confidential = 0
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 42763aed..99a34866 100755
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -29,8 +29,9 @@ print("Mr. Mojo Risin 2")
 class webqtlCaseData(object):
     """one case data in one trait"""
 
-    def __init__(self, name, value=None, variance=None, num_cases=None):
+    def __init__(self, name, value=None, variance=None, num_cases=None, name2=None):
         self.name = name
+        self.name2 = name2                  # Other name (for traits like BXD65a)
         self.value = value                  # Trait Value
         self.variance = variance            # Trait Variance
         self.num_cases = num_cases          # Number of individuals/cases
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 0358bcbf..0358bcbf 100755..100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py