Added interval_mapping to views.py

Made some more changes to interval_mapping.py

3 files changed, 82 insertions, 35 deletions

diff --git a/misc/notes.txt b/misc/notes.txt
index 91a0e67c..f6a2bb33 100644
--- a/misc/notes.txt
+++ b/misc/notes.txt
@@ -90,6 +90,9 @@ Reload web server:
 Run server:
 python runserver.py
 
+Run sendmail.py
+python send_mail.py
+
 ===========================================
 
 UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index 5d660224..aca99cbe 100644..100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -89,26 +89,56 @@ class IntervalMapping(object):
         samples, values, variances = self.trait.export_informative()
         if self.control_locus:
             if self.weighted_regression:
-                qtl_result = self.dataset.genotype.regression(strains = samples,
+                self.qtl_results = self.dataset.genotype.regression(strains = samples,
                                                               trait = values,
                                                               variance = variances,
                                                               control = self.control_locus)
             else:
-                qtl_result = self.dataset.genotype.regression(strains = samples,
+                self.qtl_results = self.dataset.genotype.regression(strains = samples,
                                                               trait = values,
                                                               control = self.control_locus)
         else:
             if self.weighted_regression:
-                qtl_result = self.dataset.genotype.regression(strains = samples,
+                self.qtl_results = self.dataset.genotype.regression(strains = samples,
                                                               trait = values,
                                                               variance = variances)
             else:
-                qtl_result = self.dataset.genotype.regression(strains = samples,
+                self.qtl_results = self.dataset.genotype.regression(strains = samples,
                                                               trait = values)
 
 
-        pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
+        #pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
+
+        #if self.dataset.group.species == "human":
+        #    p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
+        #else:
+        genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
+        
+        no_val_samples = self.identify_empty_samples()
+        trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
+        
+        genotype_matrix = np.array(trimmed_genotype_data).T
+        
+        #t_stats, p_values = lmm.run(
+        #    pheno_vector,
+        #    genotype_matrix,
+        #    restricted_max_likelihood=True,
+        #    refit=False,
+        #    temp_data=tempdata
+        #)
+        
+        #self.dataset.group.markers.add_pvalues(p_values)
+        
+        #self.qtl_results = self.dataset.group.markers.markers
 
+    def gen_qtl_results_2(self, tempdata):
+        """Generates qtl results for plotting interval map"""
+    
+        self.dataset.group.get_markers()
+        self.dataset.read_genotype_file()
+    
+        pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
+    
         #if self.dataset.group.species == "human":
         #    p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
         #else:
@@ -131,36 +161,6 @@ class IntervalMapping(object):
         
         self.qtl_results = self.dataset.group.markers.markers
 
-    #def gen_qtl_results_2(self, tempdata):
-    #    """Generates qtl results for plotting interval map"""
-    #
-    #    self.dataset.group.get_markers()
-    #    self.dataset.read_genotype_file()
-    #
-    #    pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
-    #
-    #    #if self.dataset.group.species == "human":
-    #    #    p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
-    #    #else:
-    #    genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
-    #    
-    #    no_val_samples = self.identify_empty_samples()
-    #    trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
-    #    
-    #    genotype_matrix = np.array(trimmed_genotype_data).T
-    #    
-    #    t_stats, p_values = lmm.run(
-    #        pheno_vector,
-    #        genotype_matrix,
-    #        restricted_max_likelihood=True,
-    #        refit=False,
-    #        temp_data=tempdata
-    #    )
-    #    
-    #    self.dataset.group.markers.add_pvalues(p_values)
-    #    
-    #    self.qtl_results = self.dataset.group.markers.markers
-
 
     def identify_empty_samples(self):
         no_val_samples = []
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index deccf459..29f7f150 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -32,6 +32,7 @@ from base.data_set import create_datasets_list
 from wqflask.show_trait import show_trait
 from wqflask.show_trait import export_trait_data
 from wqflask.marker_regression import marker_regression
+from wqflask.interval_mapping import interval_mapping
 from wqflask.correlation import show_corr_results
 from utility import temp_data
 
@@ -246,6 +247,49 @@ def marker_regression_page():
 
     return rendered_template
 
+@app.route("/interval_mapping", methods=('POST',))
+def interval_mapping_page():
+    initial_start_vars = request.form
+    temp_uuid = initial_start_vars['temp_uuid']
+    wanted = (
+        'trait_id',
+        'dataset',
+        'suggestive'
+    )
+
+    start_vars = {}
+    for key, value in initial_start_vars.iteritems():
+        if key in wanted or key.startswith(('value:')):
+            start_vars[key] = value
+
+    version = "v1"
+    key = "interval_mapping:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
+    print("key is:", pf(key))
+    with Bench("Loading cache"):
+        result = Redis.get(key)
+
+    if result:
+        print("Cache hit!!!")
+        with Bench("Loading results"):
+            result = pickle.loads(result)
+    else:
+        print("Cache miss!!!")
+        template_vars = interval_mapping.IntervalMapping(start_vars, temp_uuid)
+
+        template_vars.js_data = json.dumps(template_vars.js_data,
+                                           default=json_default_handler,
+                                           indent="   ")
+
+        result = template_vars.__dict__
+        
+        #causeerror
+        Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
+        Redis.expire(key, 60*60)
+
+    with Bench("Rendering template"):
+        rendered_template = render_template("interval_mapping.html", **result)
+
+    return rendered_template
 
 @app.route("/corr_compute", methods=('POST',))
 def corr_compute_page():