Remove all spacing introduced by merge

4 files changed, 32 insertions, 41 deletions

diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index bf465cdc..70ae2a1c 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -52,10 +52,10 @@ class AnonCollection(object):
         self.id = None
         self.created_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
         self.changed_timestamp = self.created_timestamp #ZS: will be updated when changes are made
-        
+
         #ZS: Find id and set it if the collection doesn't already exist
         if Redis.get(self.key) == "None" or Redis.get(self.key) == None:
-            Redis.set(self.key, None) #ZS: For some reason I get the error "Operation against a key holding the wrong kind of value" if I don't do this   
+            Redis.set(self.key, None) #ZS: For some reason I get the error "Operation against a key holding the wrong kind of value" if I don't do this
         else:
             collections_list = json.loads(Redis.get(self.key))
             collection_position = 0 #ZS: Position of collection in collection_list, if it exists
@@ -66,10 +66,10 @@ class AnonCollection(object):
                     collection_exists = True
                     self.id = collection['id']
                     break
-        
+
         if self.id == None:
             self.id = str(uuid.uuid4())
-        
+
     def get_members(self):
         traits = []
         collections_list = json.loads(Redis.get(self.key))
@@ -77,16 +77,16 @@ class AnonCollection(object):
             if collection['id'] == self.id:
                 traits = collection['members']
         return traits
-        
+
     @property
     def num_members(self):
-        num_members = 0   
+        num_members = 0
         collections_list = json.loads(Redis.get(self.key))
         for collection in collections_list:
             if collection['id'] == self.id:
                 num_members = collection['num_members']
         return num_members
-        
+
     def add_traits(self, params):
         #assert collection_name == "Default", "Unexpected collection name for anonymous user"
         self.traits = list(process_traits(params['traits']))
@@ -123,7 +123,7 @@ class AnonCollection(object):
                                "num_members" : len(self.traits),
                                "members" : self.traits}
             collections_list.append(collection_dict)
-            
+
         Redis.set(self.key, json.dumps(collections_list))
         #Redis.sadd(self.key, *list(traits))
         #Redis.expire(self.key, 60 * 60 * 24 * 5)
@@ -170,14 +170,14 @@ class UserCollection(object):
         len_before = len(members)
 
         traits = process_traits(params['traits'])
-        
+
         members_now = members
         for trait in traits:
             if trait in members:
                 continue
             else:
                 members_now.append(trait)
-              
+
         #members_now = list(members | traits)
         len_now = len(members_now)
         uc.members = json.dumps(members_now)
@@ -204,7 +204,7 @@ def process_traits(unprocessed_traits):
         assert hmac==user_manager.actual_hmac_creation(data), "Data tampering?"
         traits.add                                                                                               (str(data))
     return traits
-        
+
 def report_change(len_before, len_now):
     new_length = len_now - len_before
     if new_length:
@@ -240,7 +240,7 @@ def collections_add():
 @app.route("/collections/new")
 def collections_new():
     params = request.args
-    
+
     if "sign_in" in params:
         return redirect(url_for('login'))
 
@@ -262,10 +262,10 @@ def collections_new():
 
 def create_new(collection_name):
     params = request.args
-    
+
     unprocessed_traits = params['traits']
     traits = process_traits(unprocessed_traits)
-    
+
     if g.user_session.logged_in:
         uc = model.UserCollection()
         uc.name = collection_name
@@ -278,7 +278,7 @@ def create_new(collection_name):
     else:
         current_collections = user_manager.AnonUser().get_collections()
         ac = AnonCollection(collection_name)
-        ac.changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')       
+        ac.changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
         ac.add_traits(params)
         return redirect(url_for('view_collection', collection_id=ac.id))
 
@@ -343,7 +343,7 @@ def delete_collection():
     else:
         collection_name = params['collection_name']
         user_manager.AnonUser().delete_collection(collection_name)
-        
+
     flash("We've deleted the collection: {}.".format(collection_name), "alert-info")
 
     return redirect(url_for('list_collections'))
@@ -367,15 +367,15 @@ def view_collection():
                 break
         #this_collection = user_collections[params['collection_id']]
         traits = this_collection['members']
-                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
+
     print("in view_collection traits are:", traits)
 
     trait_obs = []
     json_version = []
 
     for atrait in traits:
-        name, dataset_name = atrait.split(':')                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
-                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
+        name, dataset_name = atrait.split(':')
+
         trait_ob = trait.GeneralTrait(name=name, dataset_name=dataset_name)
         trait_ob.retrieve_info(get_qtl_info=True)
         trait_obs.append(trait_ob)
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index c80dc700..b457b9a0 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -13,16 +13,10 @@ def run_plink(this_trait, dataset, species, vals, maf):
 
     gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = plink_output_filename)
 
-    plink_command = PLINK_COMMAND + ' --noweb --ped %s/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %s/%s.map --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (PLINK_PATH, 
-                                                                                                                                                                                                                    dataset.group.name, 
-                                                                                                                                                                                                                    PLINK_PATH, 
-                                                                                                                                                                                                                    dataset.group.name, 
-                                                                                                                                                                                                                    TMPDIR, 
-                                                                                                                                                                                                                    plink_output_filename, 
-                                                                                                                                                                                                                    this_trait.name, 
-                                                                                                                                                                                                                    maf, 
-                                                                                                                                                                                                                    TMPDIR, 
-                                                                                                                                                                                                                    plink_output_filename)
+    plink_command = PLINK_COMMAND + ' --noweb --ped %s/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %s/%s.map --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (
+        PLINK_PATH, dataset.group.name, PLINK_PATH, dataset.group.name,
+        TMPDIR, plink_output_filename, this_trait.name, maf, TMPDIR,
+        plink_output_filename)
     logger.debug("plink_command:", plink_command)
 
     os.system(plink_command)
@@ -36,7 +30,6 @@ def run_plink(this_trait, dataset, species, vals, maf):
     #        #del self.dataset.group.markers.markers[marker]
 
     logger.debug("p_values:", pf(p_values))
-
     dataset.group.markers.add_pvalues(p_values)
 
     return dataset.group.markers.markers
@@ -74,8 +67,8 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
     if new_line:
         output_file.write(new_line)
 
-    output_file.close() 
-    
+    output_file.close()
+
 # get strain name from ped file in order
 def get_samples_from_ped_file(dataset):
     ped_file= open("{}/{}.ped".format(PLINK_PATH, dataset.group.name),"r")
@@ -92,7 +85,7 @@ def get_samples_from_ped_file(dataset):
         line = ped_file.readline()
 
     return sample_list
-    
+
 def parse_plink_output(output_filename, species):
     plink_results={}
 
@@ -154,7 +147,7 @@ def parse_plink_output(output_filename, species):
     #    min_p_value = 0
 
     return count, p_value_dict
-    
+
 ######################################################
 # input: line: str,one line read from file
 # function: convert line from str to list;
@@ -165,4 +158,4 @@ def build_line_list(line=None):
     line_list = [item for item in line_list if item <>'']
     line_list = map(string.strip, line_list)
 
-    return line_list
\ No newline at end of file
+    return line_list
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index b072584c..50228b5e 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -88,6 +88,4 @@ def gen_reaper_results(this_trait, dataset, samples_before, json_data, num_perm,
         qtl = {"lrs_value": qtl.lrs, "chr":converted_chr, "Mb":reaper_locus.Mb,
                "cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive, "dominance":qtl.dominance}
         qtl_results.append(qtl)
-
-
     return qtl_results, json_data, perm_output, suggestive, significant, bootstrap_results
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index afd28563..f3694f0b 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -108,7 +108,7 @@ def geno_to_rqtl_function(dataset):        # TODO: Need to figure out why some g
          return(cross)
       }
     """ % (dataset.group.name + ".geno"))
-        
+
 def add_phenotype(cross, pheno_as_string):
     ro.globalenv["the_cross"] = cross
     ro.r('the_cross$pheno <- cbind(pull.pheno(the_cross), the_pheno = '+ pheno_as_string +')')
@@ -172,7 +172,7 @@ def process_rqtl_perm_results(num_perm, results):
     significant = np.percentile(np.array(perm_vals), 95)
 
     return perm_output, suggestive, significant
-    
+
 def process_rqtl_results(result):        # TODO: how to make this a one liner and not copy the stuff in a loop
     qtl_results = []
 
@@ -187,5 +187,5 @@ def process_rqtl_results(result):        # TODO: how to make this a one liner an
         marker['lod_score'] = output[i][2]
         qtl_results.append(marker)
 
-    return qtl_results 
-    
\ No newline at end of file
+    return qtl_results
+