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-rwxr-xr-xwqflask/base/data_set.py63
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py79
2 files changed, 74 insertions, 68 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 16f9da5d..20c9a24f 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1075,32 +1075,55 @@ class MrnaAssayDataSet(DataSet):
""" % (escape(trait), escape(self.name))
results = g.db.execute(query).fetchall()
return results
-
- def retrieve_gene_symbols(self):
- query = """
- select ProbeSet.Name, ProbeSet.Symbol, ProbeSet.GeneId
- from ProbeSet,ProbeSetXRef
- where ProbeSetXRef.ProbeSetFreezeId = %s and
- ProbeSetXRef.ProbeSetId=ProbeSet.Id;
- """ % (self.id)
- results = g.db.execute(query).fetchall()
- symbol_dict = {}
- for item in results:
- symbol_dict[item[0]] = item[1]
- return symbol_dict
- def retrieve_gene_ids(self):
+
+ def retrieve_genes(self, column_name):
query = """
- select ProbeSet.Name, ProbeSet.GeneId
+ select ProbeSet.Name, ProbeSet.%s
from ProbeSet,ProbeSetXRef
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSetXRef.ProbeSetId=ProbeSet.Id;
- """ % (self.id)
+ """ % (column_name, escape(str(self.id)))
results = g.db.execute(query).fetchall()
- symbol_dict = {}
- for item in results:
- symbol_dict[item[0]] = item[1]
- return symbol_dict
+ print("in retrieve_genes results {}: {}".format(type(results), results))
+
+ return dict(results)
+
+ #return {item[0]: item[1] for item in results}
+
+ #symbol_dict = {}
+ #for item in results:
+ # symbol_dict[item[0]] = item[1]
+ #return symbol_dict
+
+ #def retrieve_gene_symbols(self):
+ # query = """
+ # select ProbeSet.Name, ProbeSet.Symbol, ProbeSet.GeneId
+ # from ProbeSet,ProbeSetXRef
+ # where ProbeSetXRef.ProbeSetFreezeId = %s and
+ # ProbeSetXRef.ProbeSetId=ProbeSet.Id;
+ # """ % (self.id)
+ # results = g.db.execute(query).fetchall()
+ # symbol_dict = {}
+ # for item in results:
+ # symbol_dict[item[0]] = item[1]
+ # return symbol_dict
+ #
+ #def retrieve_gene_ids(self):
+ # query = """
+ # select ProbeSet.Name, ProbeSet.GeneId
+ # from ProbeSet,ProbeSetXRef
+ # where ProbeSetXRef.ProbeSetFreezeId = %s and
+ # ProbeSetXRef.ProbeSetId=ProbeSet.Id;
+ # """ % (self.id)
+ # return process_and_run_query(query)
+ # results = g.db.execute(query).fetchall()
+ # symbol_dict = {}
+ # for item in results:
+ # symbol_dict[item[0]] = item[1]
+ # return symbol_dict
+
+
class TempDataSet(DataSet):
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 5df2f316..258dcfa4 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -93,9 +93,6 @@ class CorrelationResults(object):
# get trait list from db (database name)
# calculate correlation with Base vector and targets
- #self.this_trait = GeneralTrait(dataset=self.dataset.name,
- # name=start_vars['trait_id'],
- # cellid=None)
with Bench("Doing correlations"):
helper_functions.get_species_dataset_trait(self, start_vars)
self.dataset.group.read_genotype_file()
@@ -114,9 +111,9 @@ class CorrelationResults(object):
self.dataset.group.f1list +
self.dataset.group.samplelist)
- #If either BXD/whatever Only or All Samples, append all of that group's samplelist
+ #If either BXD/whatever Only or All Samples, append all of that group's samplelist
if corr_samples_group != 'samples_other':
- self.process_samples(start_vars, primary_samples, ())
+ self.process_samples(start_vars, primary_samples)
#If either Non-BXD/whatever or All Samples, get all samples from this_trait.data and
#exclude the primary samples (because they would have been added in the previous
@@ -132,55 +129,36 @@ class CorrelationResults(object):
self.correlation_data = {}
if self.corr_type == "tissue":
- trait_symbol_dict = self.dataset.retrieve_gene_symbols()
- tissue_corr_data = self.do_tissue_correlation_for_all_traits(trait_gene_symbols = trait_symbol_dict)
- #print("tissue_corr_data: ", pf(tissue_corr_data))
+ self.trait_symbol_dict = self.dataset.retrieve_genes("Symbol")
+ tissue_corr_data = self.do_tissue_correlation_for_all_traits()
for trait in tissue_corr_data.keys()[:self.return_number]:
- self.get_sample_r_and_p_values(trait = trait, target_samples = self.target_dataset.trait_data[trait])
- #this_trait_vals = []
- #target_vals = []
- #for index, sample in enumerate(self.target_dataset.samplelist):
- # if sample in self.sample_data:
- # sample_value = self.sample_data[sample]
- # target_sample_value = self.target_dataset.trait_data[trait][index]
- # this_trait_vals.append(sample_value)
- # target_vals.append(target_sample_value)
- #
- #this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(
- # this_trait_vals, target_vals)
- #
- #if self.corr_method == 'pearson':
- # sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, target_vals)
- #else:
- # sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals)
- #
- #self.correlation_data[trait] = [sample_r, sample_p, num_overlap]
-
+ self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait])
+
elif self.corr_type == "lit":
- trait_geneid_dict = self.dataset.retrieve_gene_ids()
- lit_corr_data = self.do_lit_correlation_for_all_traits(trait_gene_ids = trait_geneid_dict)
+ self.trait_geneid_dict = self.dataset.retrieve_genes("GeneId")
+ lit_corr_data = self.do_lit_correlation_for_all_traits()
for trait in lit_corr_data.keys()[:self.return_number]:
- self.get_sample_r_and_p_values(trait = trait, target_samples = self.target_dataset.trait_data[trait])
+ self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait])
elif self.corr_type == "sample":
for trait, values in self.target_dataset.trait_data.iteritems():
- self.get_sample_r_and_p_values(trait = trait, target_samples = values)
+ self.get_sample_r_and_p_values(trait, values)
self.correlation_data = collections.OrderedDict(sorted(self.correlation_data.items(),
key=lambda t: -abs(t[1][0])))
- #print("correlation_data: ", pf(self.correlation_data))
for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
trait_object = GeneralTrait(dataset=self.dataset, name=trait, get_qtl_info=True)
-
- #print("gene symbol: ", trait_object.symbol)
- trait_object.sample_r = self.correlation_data[trait][0]
- trait_object.sample_p = self.correlation_data[trait][1]
- trait_object.num_overlap = self.correlation_data[trait][2]
+ (trait_object.sample_r,
+ trait_object.sample_p,
+ trait_object.num_overlap) = self.correlation_data[trait]
+
+ #trait_object.sample_p = self.correlation_data[trait][1]
+ #trait_object.num_overlap = self.correlation_data[trait][2]
#Get symbol for trait and call function that gets each tissue value from the database (tables TissueProbeSetXRef,
#TissueProbeSetData, etc) and calculates the correlation (cal_zero_order_corr_for_tissue in correlation_functions)
@@ -194,7 +172,6 @@ class CorrelationResults(object):
trait_object.tissue_pvalue = tissue_corr_data[trait][2]
elif self.corr_type == "lit":
trait_object.lit_corr = lit_corr_data[trait][1]
-
self.correlation_results.append(trait_object)
if self.corr_type != "lit":
@@ -305,7 +282,7 @@ class CorrelationResults(object):
#return self.correlation_results
- def do_tissue_correlation_for_all_traits(self, trait_gene_symbols, tissue_dataset_id=1):
+ def do_tissue_correlation_for_all_traits(self, tissue_dataset_id=1):
#Gets tissue expression values for the primary trait
primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list = [self.this_trait.symbol])
@@ -315,14 +292,14 @@ class CorrelationResults(object):
#print("trait_gene_symbols: ", pf(trait_gene_symbols.values()))
corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values(
- symbol_list=trait_gene_symbols.values())
+ symbol_list=self.trait_symbol_dict.values())
#print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict))
#print("trait_gene_symbols: ", pf(trait_gene_symbols))
tissue_corr_data = {}
- for trait, symbol in trait_gene_symbols.iteritems():
+ for trait, symbol in self.trait_symbol_dict.iteritems():
if symbol and symbol.lower() in corr_result_tissue_vals_dict:
this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()]
#print("this_trait_tissue_values: ", pf(this_trait_tissue_values))
@@ -375,15 +352,15 @@ class CorrelationResults(object):
trait.lit_corr = 0
- def do_lit_correlation_for_all_traits(self, trait_gene_ids):
+ def do_lit_correlation_for_all_traits(self):
input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid)
lit_corr_data = {}
- for trait, gene_id in trait_gene_ids.iteritems():
+ for trait, gene_id in self.trait_geneid_dict.iteritems():
mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), gene_id)
if mouse_gene_id and str(mouse_gene_id).find(";") == -1:
- print("gene_symbols:", input_trait_mouse_gene_id + " / " + mouse_gene_id)
+ #print("gene_symbols:", input_trait_mouse_gene_id + " / " + mouse_gene_id)
result = g.db.execute(
"""SELECT value
FROM LCorrRamin3
@@ -399,7 +376,7 @@ class CorrelationResults(object):
""" % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id))
).fetchone()
if result:
- print("result:", result)
+ #print("result:", result)
lit_corr = result.value
lit_corr_data[trait] = [gene_id, lit_corr]
else:
@@ -458,7 +435,9 @@ class CorrelationResults(object):
for index, sample in enumerate(self.target_dataset.samplelist):
if sample in self.sample_data:
sample_value = self.sample_data[sample]
+ print("sample_value:", sample_value)
target_sample_value = target_samples[index]
+ print("target_sample_value:", target_sample_value)
this_trait_vals.append(sample_value)
target_vals.append(target_sample_value)
@@ -470,7 +449,8 @@ class CorrelationResults(object):
else:
sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals)
- self.correlation_data[trait] = [sample_r, sample_p, num_overlap]
+ self.correlation_data[trait] = [sample_r, sample_p, num_overlap]
+
def do_tissue_corr_for_all_traits_2(self):
@@ -632,7 +612,10 @@ class CorrelationResults(object):
ProbeSet.Id = ProbeSetXRef.ProbeSetId order by ProbeSet.Id
"""
- def process_samples(self, start_vars, sample_names, excluded_samples):
+ def process_samples(self, start_vars, sample_names, excluded_samples=None):
+ if not excluded_samples:
+ excluded_samples = ()
+
for sample in sample_names:
if sample not in excluded_samples:
value = start_vars['value:' + sample]