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-rw-r--r--wqflask/base/data_set.py6
-rw-r--r--wqflask/base/trait.py46
-rwxr-xr-xwqflask/base/webqtlCaseData.py3
-rw-r--r--[-rwxr-xr-x]wqflask/base/webqtlConfig.py0
-rw-r--r--wqflask/wqflask/heatmap/heatmap.py2
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py28
-rw-r--r--[-rwxr-xr-x]wqflask/wqflask/show_trait/show_trait.py9
7 files changed, 34 insertions, 60 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
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 2445b37f..19c330eb 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -136,7 +136,7 @@ class Heatmap(object):
this_trait = trait_db[0]
#this_db = trait_db[1]
genotype = self.dataset.group.read_genotype_file()
- samples, values, variances = this_trait.export_informative()
+ samples, values, variances, sample_aliases = this_trait.export_informative()
trimmed_samples = []
trimmed_values = []
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 08f422f0..9cd02bd1 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -56,11 +56,21 @@ class MarkerRegression(object):
self.samples = [] # Want only ones with values
self.vals = []
-
+
+ #for sample in self.this_trait.data.keys():
for sample in self.dataset.group.samplelist:
- value = start_vars['value:' + sample]
- self.samples.append(str(sample))
- self.vals.append(value)
+ in_trait_data = False
+ for item in self.this_trait.data:
+ if self.this_trait.data[item].name2 == sample:
+ value = start_vars['value:' + self.this_trait.data[item].name]
+ self.samples.append(self.this_trait.data[item].name)
+ self.vals.append(value)
+ in_trait_data = True
+ break
+ if not in_trait_data:
+ value = start_vars['value:' + sample]
+ self.samples.append(sample)
+ self.vals.append(value)
self.mapping_method = start_vars['method']
if start_vars['manhattan_plot'] == "True":
@@ -641,15 +651,17 @@ class MarkerRegression(object):
if self.manhattan_plot != True:
genotype = genotype.addinterval()
- samples, values, variances = self.this_trait.export_informative()
-
+ samples, values, variances, sample_aliases = self.this_trait.export_informative()
+
trimmed_samples = []
trimmed_values = []
for i in range(0, len(samples)):
- if samples[i] in self.dataset.group.samplelist:
- trimmed_samples.append(samples[i])
+ if self.this_trait.data[samples[i]].name2 in self.dataset.group.samplelist:
+ trimmed_samples.append(sample_aliases[i])
trimmed_values.append(values[i])
+ #print("THE SAMPLES:", trimmed_samples)
+
if self.num_perm < 100:
self.suggestive = 0
self.significant = 0
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 074c78bf..76651cbf 100755..100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1184,17 +1184,16 @@ class ShowTrait(object):
all_samples_ordered = self.dataset.group.all_samples_ordered()
primary_sample_names = list(all_samples_ordered)
-
- print("self.dataset.group", pf(self.dataset.group.__dict__))
- print("-*- primary_samplelist is:", pf(primary_sample_names))
-
+
other_sample_names = []
for sample in this_trait.data.keys():
+ if (this_trait.data[sample].name2 in primary_sample_names) and (this_trait.data[sample].name not in primary_sample_names):
+ primary_sample_names.append(this_trait.data[sample].name)
+ primary_sample_names.remove(this_trait.data[sample].name2)
if sample not in all_samples_ordered:
all_samples_ordered.append(sample)
other_sample_names.append(sample)
- print("species:", self.dataset.group.species)
if self.dataset.group.species == "human":
primary_sample_names += other_sample_names
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 11:00:20 +0000