autopep8: Fix E20-E27

Run:
python -m autopep8 --in-place --recrusive ./ --select\
E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\
E242,E251,E252,E26,E265,E266,E27 -p 3

7 files changed, 59 insertions, 59 deletions

diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
index 12ce35e9..8eab66e8 100644
--- a/wqflask/maintenance/convert_dryad_to_bimbam.py
+++ b/wqflask/maintenance/convert_dryad_to_bimbam.py
@@ -41,7 +41,7 @@ def read_dryad_file(filename):
 
     return geno_rows
 
-    #for i, marker in enumerate(marker_list):
+    # for i, marker in enumerate(marker_list):
     #    this_row = []
     #    this_row.append(marker)
     #    this_row.append("X")
@@ -53,7 +53,7 @@ def read_dryad_file(filename):
     #        print("row: " + str(i))
     #        geno_rows.append(this_row)
     #            
-    #return geno_rows
+    # return geno_rows
 
 def write_bimbam_files(geno_rows):
     with open('/home/zas1024/cfw_data/CFW_geno.txt', 'w') as geno_fh:
@@ -64,6 +64,6 @@ def convert_dryad_to_bimbam(filename):
     geno_file_rows = read_dryad_file(filename)
     write_bimbam_files(geno_file_rows)
 
-if __name__=="__main__":
+if __name__ == "__main__":
     input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
     convert_dryad_to_bimbam(input_filename)
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index 0853b3ac..dc01cbb3 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -103,9 +103,9 @@ class ConvertGenoFile:
         with open(self.output_files[2], "w") as snp_fh:
             for marker in self.markers:
                 if self.mb_exists:
-                    snp_fh.write(marker['name'] +", " + str(int(float(marker['Mb'])*1000000)) + ", " + marker['chr'] + "\n")
+                    snp_fh.write(marker['name'] + ", " + str(int(float(marker['Mb']) * 1000000)) + ", " + marker['chr'] + "\n")
                 else:
-                    snp_fh.write(marker['name'] +", " + str(int(float(marker['cM'])*1000000)) + ", " + marker['chr'] + "\n")
+                    snp_fh.write(marker['name'] + ", " + str(int(float(marker['cM']) * 1000000)) + ", " + marker['chr'] + "\n")
 
     def get_sample_list(self, row_contents):
         self.sample_list = []
@@ -178,12 +178,12 @@ class ConvertGenoFile:
                 print("    Row is:", convertob.latest_row_value)
                 break
 
-if __name__=="__main__":
+if __name__ == "__main__":
     Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
     New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/bimbam"""
     #Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno"""
     #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps"""
     #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
-    #convertob.convert()
+    # convertob.convert()
     ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
-    #ConvertGenoFiles(Geno_Directory)
+    # ConvertGenoFiles(Geno_Directory)
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 544e2fd1..f480d63f 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -61,10 +61,10 @@ def parse_db_uri():
     parsed_uri = urllib.parse.urlparse(SQL_URI)
 
     db_conn_info = dict(
-                        db = parsed_uri.path[1:],
-                        host = parsed_uri.hostname,
-                        user = parsed_uri.username,
-                        passwd = parsed_uri.password)
+                        db=parsed_uri.path[1:],
+                        host=parsed_uri.hostname,
+                        user=parsed_uri.username,
+                        passwd=parsed_uri.password)
 
     print(db_conn_info)
     return db_conn_info
@@ -120,7 +120,7 @@ def get_types(groups):
                     if not phenotypes_exist(group_name) and not genotypes_exist(group_name):
                         types[species].pop(group_name, None)
                         groups[species] = tuple(group for group in groups[species] if group[0] != group_name)
-            else: #ZS: This whole else statement might be unnecessary, need to check
+            else:  # ZS: This whole else statement might be unnecessary, need to check
                 types_list = build_types(species, group_name)
                 if len(types_list) > 0:
                     types[species][group_name] = types_list
@@ -133,7 +133,7 @@ def get_types(groups):
 def phenotypes_exist(group_name):
     #print("group_name:", group_name)
     Cursor.execute("""select Name from PublishFreeze
-                      where PublishFreeze.Name = '%s'""" % (group_name+"Publish"))
+                      where PublishFreeze.Name = '%s'""" % (group_name + "Publish"))
 
     results = Cursor.fetchone()
     #print("RESULTS:", results)
@@ -146,7 +146,7 @@ def phenotypes_exist(group_name):
 def genotypes_exist(group_name):
     #print("group_name:", group_name)
     Cursor.execute("""select Name from GenoFreeze
-                      where GenoFreeze.Name = '%s'""" % (group_name+"Geno"))
+                      where GenoFreeze.Name = '%s'""" % (group_name + "Geno"))
 
     results = Cursor.fetchone()
     #print("RESULTS:", results)
@@ -246,7 +246,7 @@ def build_datasets(species, group, type_name):
         dataset_text = "%s Genotypes" % group
         datasets.append((dataset_id, dataset_value, dataset_text))
 
-    else: # for mRNA expression/ProbeSet
+    else:  # for mRNA expression/ProbeSet
         Cursor.execute("""select ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName from
                     ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where
                     Species.Name = '%s' and Species.Id = InbredSet.SpeciesId and
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index 3e4d1741..664e9e48 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -52,9 +52,9 @@ class GenerateKinshipMatrices:
                 break
     
     
-if __name__=="__main__":
+if __name__ == "__main__":
     Geno_Directory = """/export/local/home/zas1024/genotype_files/genotype/"""
     Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/"""
     GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory)
     
-    #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD
+    # ./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index f5f7e0e7..fa0dcebd 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -66,16 +66,16 @@ class ConvertGenoFile:
         self.configurations = {}
         #self.skipped_cols = 3
         
-        #if self.input_file.endswith(".geno.gz"):
+        # if self.input_file.endswith(".geno.gz"):
         #    print("self.input_file: ", self.input_file)
         #    self.input_fh = gzip.open(self.input_file)
-        #else:
+        # else:
         self.input_fh = open(self.input_file)
         
         with open(self.output_file, "w") as self.output_fh:
-            #if self.file_type == "geno":
+            # if self.file_type == "geno":
             self.process_csv()
-            #elif self.file_type == "snps":
+            # elif self.file_type == "snps":
             #    self.process_snps_file()
 
 
@@ -105,7 +105,7 @@ class ConvertGenoFile:
                     this_marker.genotypes.append("NA")
                 
             #print("this_marker is:", pf(this_marker.__dict__))   
-            #if this_marker.chr == "14":
+            # if this_marker.chr == "14":
             self.markers.append(this_marker.__dict__)
 
         with open(self.output_file, 'w') as fh:
@@ -115,16 +115,16 @@ class ConvertGenoFile:
                 #self.latest_col_pos = item_count + self.skipped_cols
                 #self.latest_col_value = item
                 
-                #if item_count != 0:
+                # if item_count != 0:
                 #    self.output_fh.write(" ")
-                #self.output_fh.write(self.configurations[item.upper()])
+                # self.output_fh.write(self.configurations[item.upper()])
                     
-            #self.output_fh.write("\n")
+            # self.output_fh.write("\n")
 
 
     def process_rows(self):
         for self.latest_row_pos, row in enumerate(self.input_fh):
-            #if self.input_file.endswith(".geno.gz"):
+            # if self.input_file.endswith(".geno.gz"):
             #    print("row: ", row)
             self.latest_row_value = row
             # Take care of headers
@@ -176,21 +176,21 @@ class ConvertGenoFile:
                 print("    Row is:", convertob.latest_row_value)
                 break
             
-    #def process_snps_file(cls, snps_file, new_directory):
+    # def process_snps_file(cls, snps_file, new_directory):
     #    output_file = os.path.join(new_directory, "mouse_families.json")
     #    print("%s -> %s" % (snps_file, output_file))
     #    convertob = ConvertGenoFile(input_file, output_file)
         
 
 
-if __name__=="__main__":
+if __name__ == "__main__":
     Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
     New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/json"""
     #Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno"""
     #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps"""
     #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
-    #convertob.convert()
+    # convertob.convert()
     ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
-    #ConvertGenoFiles(Geno_Directory)
+    # ConvertGenoFiles(Geno_Directory)
     
     #process_csv(Input_File, Output_File)
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 701b2b50..6751a8e5 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -20,10 +20,10 @@ def parse_db_uri():
     parsed_uri = urllib.parse.urlparse(SQL_URI)
 
     db_conn_info = dict(
-                        db = parsed_uri.path[1:],
-                        host = parsed_uri.hostname,
-                        user = parsed_uri.username,
-                        passwd = parsed_uri.password)
+                        db=parsed_uri.path[1:],
+                        host=parsed_uri.hostname,
+                        user=parsed_uri.username,
+                        passwd=parsed_uri.password)
 
     print(db_conn_info)
     return db_conn_info
@@ -35,16 +35,16 @@ def create_dataframe(input_file):
     input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols)))
     return pd.DataFrame(input_array)
 
-#This function taken from https://github.com/ShawnLYU/Quantile_Normalize
+# This function taken from https://github.com/ShawnLYU/Quantile_Normalize
 def quantileNormalize(df_input):
     df = df_input.copy()
-    #compute rank
+    # compute rank
     dic = {}
     for col in df:
-        dic.update({col : sorted(df[col])})
+        dic.update({col: sorted(df[col])})
     sorted_df = pd.DataFrame(dic)
-    rank = sorted_df.mean(axis = 1).tolist()
-    #sort
+    rank = sorted_df.mean(axis=1).tolist()
+    # sort
     for col in df:
         t = np.searchsorted(np.sort(df[col]), df[col])
         df[col] = [rank[i] for i in t]
@@ -65,8 +65,8 @@ def set_data(dataset_name):
                 for i, sample in enumerate(sample_names):
                     this_sample = {
                                     "name": sample,
-                                    "value": line1.split('\t')[i+1],
-                                    "qnorm": line2.split('\t')[i+1]
+                                    "value": line1.split('\t')[i + 1],
+                                    "qnorm": line2.split('\t')[i + 1]
                                   }
                     sample_list.append(this_sample)
                 query = """SELECT Species.SpeciesName, InbredSet.InbredSetName, ProbeSetFreeze.FullName
@@ -99,9 +99,9 @@ if __name__ == '__main__':
     Conn = MySQLdb.Connect(**parse_db_uri())
     Cursor = Conn.cursor()
 
-    #es = Elasticsearch([{
+    # es = Elasticsearch([{
     #    "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
-    #}], timeout=60) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
+    # }], timeout=60) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
 
     es = get_elasticsearch_connection(for_user=False)
 
@@ -116,8 +116,8 @@ if __name__ == '__main__':
     success, _ = bulk(es, set_data(sys.argv[1]))
 
     response = es.search(
-        index = "traits", doc_type = "trait", body = {
-            "query": { "match": { "name": "ENSMUSG00000028982" } }
+        index="traits", doc_type="trait", body = {
+            "query": {"match": {"name": "ENSMUSG00000028982"}}
         }
     )
 
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 4177c124..286094dd 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -43,10 +43,10 @@ def parse_db_uri():
     parsed_uri = urllib.parse.urlparse(SQL_URI)
 
     db_conn_info = dict(
-                        db = parsed_uri.path[1:],
-                        host = parsed_uri.hostname,
-                        user = parsed_uri.username,
-                        passwd = parsed_uri.password)
+                        db=parsed_uri.path[1:],
+                        host=parsed_uri.hostname,
+                        user=parsed_uri.username,
+                        passwd=parsed_uri.password)
 
     print(db_conn_info)
     return db_conn_info
@@ -63,14 +63,14 @@ def insert_probeset_resources(default_owner_id):
         resource_ob = {}
         resource_ob['name'] = resource[1]
         resource_ob['owner_id'] = default_owner_id
-        resource_ob['data'] = { "dataset" : str(resource[0])}
+        resource_ob['data'] = {"dataset": str(resource[0])}
         resource_ob['type'] = "dataset-probeset"
         if resource[2] < 1 and resource[3] > 0:
-            resource_ob['default_mask'] = { "data": "view",
+            resource_ob['default_mask'] = {"data": "view",
                                             "metadata": "view",
                                             "admin": "not-admin"}
         else:
-            resource_ob['default_mask'] = { "data": "no-access",
+            resource_ob['default_mask'] = {"data": "no-access",
                                             "metadata": "no-access",
                                             "admin": "not-admin"}
         resource_ob['group_masks'] = {}
@@ -97,10 +97,10 @@ def insert_publish_resources(default_owner_id):
             else:
                 resource_ob['name'] = str(resource[0])
             resource_ob['owner_id'] = default_owner_id
-            resource_ob['data'] = { "dataset" : str(resource[1]) ,
-                                    "trait"   : str(resource[0])}
+            resource_ob['data'] = {"dataset": str(resource[1]),
+                                    "trait": str(resource[0])}
             resource_ob['type'] = "dataset-publish"
-            resource_ob['default_mask'] = { "data": "view",
+            resource_ob['default_mask'] = {"data": "view",
                                             "metadata": "view",
                                             "admin": "not-admin"}
 
@@ -125,14 +125,14 @@ def insert_geno_resources(default_owner_id):
             resource_ob['owner_id'] = "c5ce8c56-78a6-474f-bcaf-7129d97f56ae"
         else:
             resource_ob['owner_id'] = default_owner_id
-        resource_ob['data'] = { "dataset" : str(resource[0]) }
+        resource_ob['data'] = {"dataset": str(resource[0])}
         resource_ob['type'] = "dataset-geno"
         if resource[2] < 1:
-            resource_ob['default_mask'] = { "data": "view",
+            resource_ob['default_mask'] = {"data": "view",
                                             "metadata": "view",
                                             "admin": "not-admin"}
         else:
-            resource_ob['default_mask'] = { "data": "no-access",
+            resource_ob['default_mask'] = {"data": "no-access",
                                             "metadata": "no-access",
                                             "admin": "not-admin"}
         resource_ob['group_masks'] = {}