autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133

6 files changed, 34 insertions, 34 deletions

diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index c5af1ca6..078be529 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -56,7 +56,7 @@ class ConvertGenoFile:
             '@pat': "0",
             '@het': "0.5",
             '@unk': "NA"
-            }
+        }
 
         self.configurations = {}
         self.input_fh = open(self.input_file)
@@ -171,7 +171,7 @@ class ConvertGenoFile:
             snp_output_file = os.path.join(
                 new_directory, group_name + "_snps.txt")
             output_files = [geno_output_file,
-                pheno_output_file, snp_output_file]
+                            pheno_output_file, snp_output_file]
             print("%s -> %s" % (
                 os.path.join(old_directory, input_file), geno_output_file))
             convertob = ConvertGenoFile(input_file, output_files)
@@ -184,7 +184,7 @@ class ConvertGenoFile:
                 print("  Exception:", why)
                 print(traceback.print_exc())
                 print("    Found in row %s at tabular column %s" % (convertob.latest_row_pos,
-                                                                convertob.latest_col_pos))
+                                                                    convertob.latest_col_pos))
                 print("    Column is:", convertob.latest_col_value)
                 print("    Row is:", convertob.latest_row_value)
                 break
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 484336a6..db65a11f 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -62,10 +62,10 @@ 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
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index cd39fceb..9f01d094 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -23,7 +23,7 @@ class GenerateKinshipMatrices:
     def generate_kinship(self):
         gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + \
             " -p " + self.pheno_file + \
-                " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name
+            " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name
         print("command:", gemma_command)
         os.system(gemma_command)
 
@@ -52,7 +52,7 @@ class GenerateKinshipMatrices:
                 print("  Exception:", why)
                 print(traceback.print_exc())
                 print("    Found in row %s at tabular column %s" % (convertob.latest_row_pos,
-                                                                convertob.latest_col_pos))
+                                                                    convertob.latest_col_pos))
                 print("    Column is:", convertob.latest_col_value)
                 print("    Row is:", convertob.latest_row_value)
                 break
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index c74489a8..32e0e34b 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -63,7 +63,7 @@ class ConvertGenoFile:
             '@pat': "0",
             '@het': "0.5",
             '@unk': "NA"
-            }
+        }
 
         self.configurations = {}
         #self.skipped_cols = 3
@@ -172,7 +172,7 @@ class ConvertGenoFile:
                 print("  Exception:", why)
                 print(traceback.print_exc())
                 print("    Found in row %s at tabular column %s" % (convertob.latest_row_pos,
-                                                                convertob.latest_col_pos))
+                                                                    convertob.latest_col_pos))
                 print("    Column is:", convertob.latest_col_value)
                 print("    Row is:", convertob.latest_row_value)
                 break
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index ac7689f5..88bb2cb5 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -21,10 +21,10 @@ 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
@@ -70,10 +70,10 @@ def set_data(dataset_name):
                 trait_name = line1.split('\t')[0]
                 for i, sample in enumerate(sample_names):
                     this_sample = {
-                                    "name": sample,
-                                    "value": line1.split('\t')[i + 1],
-                                    "qnorm": line2.split('\t')[i + 1]
-                                  }
+                        "name": sample,
+                        "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
                            FROM Species, InbredSet, ProbeSetFreeze, ProbeFreeze, ProbeSetXRef, ProbeSet
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index c6c4f44c..0f472494 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -44,10 +44,10 @@ 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
@@ -69,12 +69,12 @@ def insert_probeset_resources(default_owner_id):
         resource_ob['type'] = "dataset-probeset"
         if resource[2] < 1 and resource[3] > 0:
             resource_ob['default_mask'] = {"data": "view",
-                                            "metadata": "view",
-                                            "admin": "not-admin"}
+                                           "metadata": "view",
+                                           "admin": "not-admin"}
         else:
             resource_ob['default_mask'] = {"data": "no-access",
-                                            "metadata": "no-access",
-                                            "admin": "not-admin"}
+                                           "metadata": "no-access",
+                                           "admin": "not-admin"}
         resource_ob['group_masks'] = {}
 
         add_resource(resource_ob, update=False)
@@ -101,11 +101,11 @@ def insert_publish_resources(default_owner_id):
                 resource_ob['name'] = str(resource[0])
             resource_ob['owner_id'] = default_owner_id
             resource_ob['data'] = {"dataset": str(resource[1]),
-                                    "trait": str(resource[0])}
+                                   "trait": str(resource[0])}
             resource_ob['type'] = "dataset-publish"
             resource_ob['default_mask'] = {"data": "view",
-                                            "metadata": "view",
-                                            "admin": "not-admin"}
+                                           "metadata": "view",
+                                           "admin": "not-admin"}
 
             resource_ob['group_masks'] = {}
 
@@ -133,12 +133,12 @@ def insert_geno_resources(default_owner_id):
         resource_ob['type'] = "dataset-geno"
         if resource[2] < 1:
             resource_ob['default_mask'] = {"data": "view",
-                                            "metadata": "view",
-                                            "admin": "not-admin"}
+                                           "metadata": "view",
+                                           "admin": "not-admin"}
         else:
             resource_ob['default_mask'] = {"data": "no-access",
-                                            "metadata": "no-access",
-                                            "admin": "not-admin"}
+                                           "metadata": "no-access",
+                                           "admin": "not-admin"}
         resource_ob['group_masks'] = {}
 
         add_resource(resource_ob, update=False)