autopep8: Run autopep8 100 times with target rules

Rules used are:
E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242,
E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306,
E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121,
E122,E123,E124,E125,E126,E127,E128,E129,E131,E133

28 files changed, 172 insertions, 164 deletions

diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 872b52eb..39947158 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -15,7 +15,7 @@ from utility.tools import valid_path, mk_dir, assert_dir, assert_writable_dir, f
 DEBUG = 1
 
 # USER privilege
-USERDICT = {'guest': 1, 'user': 2, 'admin': 3, 'root':4}
+USERDICT = {'guest': 1, 'user': 2, 'admin': 3, 'root': 4}
 
 # Set privileges
 SUPER_PRIVILEGES = {'data': 'edit', 'metadata': 'edit', 'admin': 'edit-admins'}
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 88bb2cb5..0cc963e5 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -123,7 +123,7 @@ if __name__ == '__main__':
     success, _ = bulk(es, set_data(sys.argv[1]))
 
     response = es.search(
-        index="traits", doc_type="trait", body = {
+        index="traits", doc_type="trait", body={
             "query": {"match": {"name": "ENSMUSG00000028982"}}
         }
     )
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index 93848a84..8b4337ec 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -9,13 +9,14 @@ from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
 class TestQtlReaperMapping(unittest.TestCase):
     @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
     def test_gen_pheno_txt_file(self):
-        vals = ["V1", "x", "V4", "V3","x"]
-        samples = ["S1", "S2", "S3", "S4","S5"]
+        vals = ["V1", "x", "V4", "V3", "x"]
+        samples = ["S1", "S2", "S3", "S4", "S5"]
         trait_filename = "trait_file"
         with mock.patch("builtins.open", mock.mock_open())as mock_open:
             gen_pheno_txt_file(samples=samples, vals=vals,
                                trait_filename=trait_filename)
-            mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w")
+            mock_open.assert_called_once_with(
+                "/home/user/data/gn2/trait_file.txt", "w")
             filehandler = mock_open()
             write_calls = [mock.call('Trait\t'), mock.call(
                 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index 68686e27..91d2c587 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -28,7 +28,7 @@ class TestRqtlMapping(unittest.TestCase):
 
     def test_sanitize_rqtl_phenotype(self):
         """test for sanitizing rqtl phenotype"""
-        vals = ['f', "x", "r", "x","x"]
+        vals = ['f', "x", "r", "x", "x"]
         results = sanitize_rqtl_phenotype(vals)
         expected_phenotype_string = 'c(f,NA,r,NA,NA)'
 
@@ -36,7 +36,7 @@ class TestRqtlMapping(unittest.TestCase):
 
     def test_sanitize_rqtl_names(self):
         """test for sanitzing rqtl names"""
-        vals = ['f', "x", "r", "x","x"]
+        vals = ['f', "x", "r", "x", "x"]
         expected_sanitized_name = "c('f',NA,'r',NA,NA)"
         results = sanitize_rqtl_names(vals)
         self.assertEqual(expected_sanitized_name, results)
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 37a8a1a5..9b2c6735 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -188,7 +188,8 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
     for i in range(int(stepX) + 1):
         xc = xLeftOffset + (x - xLow) * xScale
         im_drawer.line(
-            xy=((xc, yTopOffset + plotHeight), (xc, yTopOffset + plotHeight + 5)),
+            xy=((xc, yTopOffset + plotHeight),
+                (xc, yTopOffset + plotHeight + 5)),
             fill=axesColor)
         strX = cformat(d=x, rank=0)
         im_drawer.text(
@@ -217,7 +218,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
             text=XLabel,
             xy=(xLeftOffset + (
                 plotWidth - im_drawer.textsize(XLabel, font=labelFont)[0]) / 2.0,
-                yTopOffset + plotHeight + yBottomOffset-10),
+                yTopOffset + plotHeight + yBottomOffset - 10),
             font=labelFont, fill=labelColor)
 
     if YLabel:
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index e56c22eb..eae3ba03 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -105,7 +105,7 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
     item_details = None
     try:
         response = es.search(
-            index=index, doc_type=doc_type, body = {
+            index=index, doc_type=doc_type, body={
                 "query": {"match": {column_name: column_value}}
             })
         if len(response["hits"]["hits"]) > 0:
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index bc3bc833..eddb97da 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -229,13 +229,13 @@ class pathdata:
 
     def bezier(self, x1, y1, x2, y2, x, y):
         """bezier with xy1 and xy2 to xy absolut"""
-        self.path.append('C' + str(x1) + ','+str(y1)+' '+str(x2)
-                         + ',' + str(y2) + ' '+str(x)+','+str(y))
+        self.path.append('C' + str(x1) + ',' + str(y1) + ' ' + str(x2)
+                         + ',' + str(y2) + ' ' + str(x) + ',' + str(y))
 
     def relbezier(self, x1, y1, x2, y2, x, y):
         """bezier with xy1 and xy2 to xy relative"""
-        self.path.append('c' + str(x1) + ','+str(y1)+' '+str(x2)
-                         + ',' + str(y2) + ' '+str(x)+','+str(y))
+        self.path.append('c' + str(x1) + ',' + str(y1) + ' ' + str(x2)
+                         + ',' + str(y2) + ' ' + str(x) + ',' + str(y))
 
     def smbezier(self, x2, y2, x, y):
         """smooth bezier with xy2 to xy absolut"""
@@ -267,13 +267,13 @@ class pathdata:
 
     def ellarc(self, rx, ry, xrot, laf, sf, x, y):
         """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag  to xy absolut"""
-        self.path.append('A' + str(rx) + ','+str(ry)+' '+str(xrot)
-                         + ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
+        self.path.append('A' + str(rx) + ',' + str(ry) + ' ' + str(xrot)
+                         + ' ' + str(laf) + ' ' + str(sf) + ' ' + str(x) + ' ' + str(y))
 
     def relellarc(self, rx, ry, xrot, laf, sf, x, y):
         """elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag  to xy relative"""
-        self.path.append('a' + str(rx) + ','+str(ry)+' '+str(xrot)
-                         + ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
+        self.path.append('a' + str(rx) + ',' + str(ry) + ' ' + str(xrot)
+                         + ' ' + str(laf) + ' ' + str(sf) + ' ' + str(x) + ' ' + str(y))
 
     def __repr__(self):
         return ' '.join(self.path)
@@ -471,7 +471,7 @@ class ellipse(SVGelement):
     an ellipse is defined as a center and a x and y radius.
     """
 
-    def __init__(self, cx=None, cy=None, rx=None, ry=None,fill=None,stroke=None,stroke_width=None,**args):
+    def __init__(self, cx=None, cy=None, rx=None, ry=None, fill=None, stroke=None, stroke_width=None, **args):
         if rx == None or ry == None:
             raise ValueError('both rx and ry are required')
 
@@ -494,7 +494,7 @@ class circle(SVGelement):
     The circle creates an element using a x, y and radius values eg
     """
 
-    def __init__(self, cx=None, cy=None, r=None, fill=None,stroke=None,stroke_width=None,**args):
+    def __init__(self, cx=None, cy=None, r=None, fill=None, stroke=None, stroke_width=None, **args):
         if r == None:
             raise ValueError('r is required')
         SVGelement.__init__(self, 'circle', {'r': r}, **args)
@@ -527,7 +527,7 @@ class line(SVGelement):
     A line is defined by a begin x,y pair and an end x,y pair
     """
 
-    def __init__(self, x1=None, y1=None, x2=None, y2=None,stroke=None,stroke_width=None,**args):
+    def __init__(self, x1=None, y1=None, x2=None, y2=None, stroke=None, stroke_width=None, **args):
         SVGelement.__init__(self, 'line', **args)
         if x1 != None:
             self.attributes['x1'] = x1
@@ -549,7 +549,7 @@ class polyline(SVGelement):
     a polyline is defined by a list of xy pairs
     """
 
-    def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
+    def __init__(self, points, fill=None, stroke=None, stroke_width=None, **args):
         SVGelement.__init__(self, 'polyline', {
                             'points': _xypointlist(points)}, **args)
         if fill != None:
@@ -566,7 +566,7 @@ class polygon(SVGelement):
     a polygon is defined by a list of xy pairs
     """
 
-    def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
+    def __init__(self, points, fill=None, stroke=None, stroke_width=None, **args):
         SVGelement.__init__(
             self, 'polygon', {'points': _xypointlist(points)}, **args)
         if fill != None:
@@ -583,7 +583,7 @@ class path(SVGelement):
     a path is defined by a path object and optional width, stroke and fillcolor
     """
 
-    def __init__(self, pathdata, fill=None, stroke=None, stroke_width=None,id=None,**args):
+    def __init__(self, pathdata, fill=None, stroke=None, stroke_width=None, id=None, **args):
         SVGelement.__init__(self, 'path', {'d': str(pathdata)}, **args)
         if stroke != None:
             self.attributes['stroke'] = stroke
@@ -601,7 +601,7 @@ class text(SVGelement):
     a text element can bge used for displaying text on the screen
     """
 
-    def __init__(self, x=None, y=None, text=None, font_size=None,font_family=None,text_anchor=None,**args):
+    def __init__(self, x=None, y=None, text=None, font_size=None, font_family=None, text_anchor=None, **args):
         SVGelement.__init__(self, 'text', **args)
         if x != None:
             self.attributes['x'] = x
@@ -637,7 +637,7 @@ class pattern(SVGelement):
     in x and y to cover the areas to be painted.
     """
 
-    def __init__(self, x=None, y=None, width=None, height=None,patternUnits=None,**args):
+    def __init__(self, x=None, y=None, width=None, height=None, patternUnits=None, **args):
         SVGelement.__init__(self, 'pattern', **args)
         if x != None:
             self.attributes['x'] = x
@@ -684,7 +684,7 @@ class lineargradient(SVGelement):
     stop elements van be added to define the gradient colors.
     """
 
-    def __init__(self, x1=None, y1=None, x2=None, y2=None,id=None,**args):
+    def __init__(self, x1=None, y1=None, x2=None, y2=None, id=None, **args):
         SVGelement.__init__(self, 'linearGradient', **args)
         if x1 != None:
             self.attributes['x1'] = x1
@@ -705,7 +705,7 @@ class radialgradient(SVGelement):
     stop elements van be added to define the gradient colors.
     """
 
-    def __init__(self, cx=None, cy=None, r=None, fx=None,fy=None,id=None,**args):
+    def __init__(self, cx=None, cy=None, r=None, fx=None, fy=None, id=None, **args):
         SVGelement.__init__(self, 'radialGradient', **args)
         if cx != None:
             self.attributes['cx'] = cx
@@ -749,11 +749,11 @@ class image(SVGelement):
     adds an image to the drawing. Supported formats are .png, .jpg and .svg.
     """
 
-    def __init__(self, url, x=None, y=None, width=None,height=None,**args):
+    def __init__(self, url, x=None, y=None, width=None, height=None, **args):
         if width == None or height == None:
             raise ValueError('both height and width are required')
         SVGelement.__init__(
-            self, 'image', {'xlink:href': url, 'width': width, 'height':height}, **args)
+            self, 'image', {'xlink:href': url, 'width': width, 'height': height}, **args)
         if x != None:
             self.attributes['x'] = x
         if y != None:
@@ -777,7 +777,7 @@ class marker(SVGelement):
     add an element to it which should be used as a marker.
     """
 
-    def __init__(self, id=None, viewBox=None, refx=None, refy=None,markerWidth=None,markerHeight=None,**args):
+    def __init__(self, id=None, viewBox=None, refx=None, refy=None, markerWidth=None, markerHeight=None, **args):
         SVGelement.__init__(self, 'marker', **args)
         if id != None:
             self.attributes['id'] = id
@@ -851,7 +851,7 @@ class use(SVGelement):
     references a symbol by linking to its id and its position, height and width
     """
 
-    def __init__(self, link, x=None, y=None, width=None,height=None,**args):
+    def __init__(self, link, x=None, y=None, width=None, height=None, **args):
         SVGelement.__init__(self, 'use', {'xlink:href': link}, **args)
         if x != None:
             self.attributes['x'] = x
@@ -904,7 +904,7 @@ class animate(SVGelement):
     animates an attribute.
     """
 
-    def __init__(self, attribute, fr=None, to=None, dur=None,**args):
+    def __init__(self, attribute, fr=None, to=None, dur=None, **args):
         SVGelement.__init__(
             self, 'animate', {'attributeName': attribute}, **args)
         if fr != None:
@@ -935,7 +935,7 @@ class animateTransform(SVGelement):
     transform an element from and to a value.
     """
 
-    def __init__(self, type=None, fr=None, to=None, dur=None,**args):
+    def __init__(self, type=None, fr=None, to=None, dur=None, **args):
         SVGelement.__init__(self, 'animateTransform', {
                             'attributeName': 'transform'}, **args)
         # As far as I know the attributeName is always transform
@@ -955,7 +955,7 @@ class animateColor(SVGelement):
     Animates the color of a element
     """
 
-    def __init__(self, attribute, type=None, fr=None, to=None,dur=None,**args):
+    def __init__(self, attribute, type=None, fr=None, to=None, dur=None, **args):
         SVGelement.__init__(self, 'animateColor', {
                             'attributeName': attribute}, **args)
         if type != None:
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index cbef96eb..f8b0d8bd 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -53,7 +53,8 @@ def do_mapping_for_api(start_vars):
         header_row = ["name", "chr", "cM", "lod_score"]
         if mapping_params['num_perm'] > 0:
             _sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'],
-                                                                                                  mapping_params['perm_check'], mapping_params['num_perm'],
+                                                                                                  mapping_params['perm_check'], mapping_params[
+                                                                                                      'num_perm'],
                                                                                                   mapping_params['do_control'], mapping_params[
                 'control_marker'],
                 mapping_params['manhattan_plot'], mapping_params['pair_scan'])
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 9d3446db..aec74c9e 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -98,8 +98,8 @@ def get_groups_list(species_name=None):
                 "Name": group[3],
                 "FullName": group[4],
                 "public": group[5],
-              "MappingMethodId": group[6],
-              "GeneticType": group[7]
+                "MappingMethodId": group[6],
+                "GeneticType": group[7]
             }
             groups_list.append(group_dict)
 
@@ -143,8 +143,8 @@ def get_group_info(group_name, species_name=None, file_format="json"):
             "Name": group[3],
             "FullName": group[4],
             "public": group[5],
-          "MappingMethodId": group[6],
-          "GeneticType": group[7]
+            "MappingMethodId": group[6],
+            "GeneticType": group[7]
         }
 
         return flask.jsonify(group_dict)
@@ -192,11 +192,11 @@ def get_datasets_for_group(group_name, species_name=None):
                 "Short_Abbreviation": dataset[3],
                 "Long_Abbreviation": dataset[4],
                 "FullName": dataset[5],
-              "ShortName": dataset[6],
-              "CreateTime": dataset[7],
-              "public": dataset[8],
-              "confidentiality": dataset[9],
-              "DataScale": dataset[10]
+                "ShortName": dataset[6],
+                "CreateTime": dataset[7],
+                "public": dataset[8],
+                "confidentiality": dataset[9],
+                "DataScale": dataset[10]
             }
             datasets_list.append(dataset_dict)
 
@@ -249,10 +249,10 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"):
             "full_name": dataset[2],
             "short_name": dataset[3],
             "data_scale": dataset[4],
-          "tissue_id": dataset[5],
-          "tissue": dataset[6],
-          "public": dataset[7],
-          "confidential": dataset[8]
+            "tissue_id": dataset[5],
+            "tissue": dataset[6],
+            "public": dataset[7],
+            "confidential": dataset[8]
         }
 
         datasets_list.append(dataset_dict)
@@ -286,7 +286,7 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"):
                     "description": dataset[2],
                     "pubmed_id": dataset[5],
                     "title": dataset[6],
-                  "year": dataset[7]
+                    "year": dataset[7]
                 }
             elif dataset[4]:
                 dataset_dict = {
@@ -777,7 +777,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
                         i += 1
 
             csv_writer = csv.writer(
-                si, delimiter="\t", escapechar="\\", quoting = csv.QUOTE_NONE)
+                si, delimiter="\t", escapechar="\\", quoting=csv.QUOTE_NONE)
         else:
             return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
     elif file_format == "rqtl2":
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 58518639..01274ba9 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -77,13 +77,13 @@ def collections_add():
         return render_template("collections/add.html",
                                traits=traits,
                                collections=collections,
-                              )
+                               )
     else:
         hash = request.args['hash']
         return render_template("collections/add.html",
                                hash=hash,
                                collections=collections,
-                              )
+                               )
 
 
 @app.route("/collections/new")
@@ -147,7 +147,7 @@ def list_collections():
     return render_template("collections/list.html",
                            params=params,
                            collections=user_collections,
-                            )
+                           )
 
 
 @app.route("/collections/remove", methods=('POST',))
@@ -226,7 +226,7 @@ def view_collection():
     else:
         return render_template("collections/view.html",
                                **collection_info
-                           )
+                               )
 
 
 @app.route("/collections/change_name", methods=('POST',))
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 4f756f58..cafb9265 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -18,12 +18,12 @@ class CorrScatterPlot:
     def __init__(self, params):
         if "Temp" in params['dataset_1']:
             self.dataset_1 = data_set.create_dataset(
-                dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_1'].split("_")[1])
+                dataset_name="Temp", dataset_type="Temp", group_name=params['dataset_1'].split("_")[1])
         else:
             self.dataset_1 = data_set.create_dataset(params['dataset_1'])
         if "Temp" in params['dataset_2']:
             self.dataset_2 = data_set.create_dataset(
-                dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_2'].split("_")[1])
+                dataset_name="Temp", dataset_type="Temp", group_name=params['dataset_2'].split("_")[1])
         else:
             self.dataset_2 = data_set.create_dataset(params['dataset_2'])
 
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index aa39bc5c..9b0b6118 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -79,7 +79,7 @@ class CorrelationResults:
         with Bench("Doing correlations"):
             if start_vars['dataset'] == "Temp":
                 self.dataset = data_set.create_dataset(
-                    dataset_name="Temp", dataset_type="Temp", group_name = start_vars['group'])
+                    dataset_name="Temp", dataset_type="Temp", group_name=start_vars['group'])
                 self.trait_id = start_vars['trait_id']
                 self.this_trait = create_trait(dataset=self.dataset,
                                                name=self.trait_id,
@@ -609,14 +609,14 @@ def get_header_fields(data_type, corr_method):
                              'Location',
                              'Mean',
                              'Sample rho',
-                                'N',
-                                'Sample p(rho)',
-                                'Lit rho',
-                                'Tissue rho',
-                                'Tissue p(rho)',
-                                'Max LRS',
-                                'Max LRS Location',
-                                'Additive Effect']
+                             'N',
+                             'Sample p(rho)',
+                             'Lit rho',
+                             'Tissue rho',
+                             'Tissue p(rho)',
+                             'Max LRS',
+                             'Max LRS Location',
+                             'Additive Effect']
         else:
             header_fields = ['Index',
                              'Record',
@@ -625,14 +625,14 @@ def get_header_fields(data_type, corr_method):
                              'Location',
                              'Mean',
                              'Sample r',
-                                'N',
-                                'Sample p(r)',
-                                'Lit r',
-                                'Tissue r',
-                                'Tissue p(r)',
-                                'Max LRS',
-                                'Max LRS Location',
-                                'Additive Effect']
+                             'N',
+                             'Sample p(r)',
+                             'Lit r',
+                             'Tissue r',
+                             'Tissue p(r)',
+                             'Max LRS',
+                             'Max LRS Location',
+                             'Additive Effect']
     elif data_type == "Publish":
         if corr_method == "spearman":
             header_fields = ['Index',
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index c1bf3daa..3a54a218 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -211,7 +211,7 @@ class CorrelationMatrix:
 
         this_group_name = self.trait_list[0][1].group.name
         temp_dataset = data_set.create_dataset(
-            dataset_name="Temp", dataset_type="Temp", group_name = this_group_name)
+            dataset_name="Temp", dataset_type="Temp", group_name=this_group_name)
         temp_dataset.group.get_samplelist()
         for i, pca_trait in enumerate(pca_traits):
             trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + \
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index a0fb34d8..bb928ec5 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -154,7 +154,7 @@ class CTL:
 
         # Perform the CTL scan
         res = self.r_CTLscan(rGeno, rPheno, strategy=strategy,
-                             nperm=nperm, parametric = parametric, nthreads=6)
+                             nperm=nperm, parametric=parametric, nthreads=6)
 
         # Get significant interactions
         significant = self.r_CTLsignificant(res, significance=significance)
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index b7e7e38a..04a100ba 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -120,14 +120,16 @@ def add_or_edit_group():
         if "admin_emails_to_add" in params:
             admin_emails = params['admin_emails_to_add'].split(",")
             for email in admin_emails:
-                user_details = get_user_by_unique_column("email_address", email)
+                user_details = get_user_by_unique_column(
+                    "email_address", email)
                 if user_details:
                     admin_user_ids.add(user_details['user_id'])
             #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins")
         if "member_emails_to_add" in params:
             member_emails = params['member_emails_to_add'].split(",")
             for email in member_emails:
-                user_details = get_user_by_unique_column("email_address", email)
+                user_details = get_user_by_unique_column(
+                    "email_address", email)
                 if user_details:
                     member_user_ids.add(user_details['user_id'])
             #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members")
@@ -156,7 +158,7 @@ def send_group_invites(group_id, user_email_list=[], user_type="members"):
                     continue
                 else:
                     send_verification_email(user_details, template_name="email/group_verification.txt",
-                                            key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group")
+                                            key_prefix="verification_code", subject="You've been invited to join a GeneNetwork user group")
         else:
             temp_password = ''.join(random.choice(
                 string.ascii_uppercase + string.digits) for _ in range(6))
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 04980281..5e86ae31 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -60,7 +60,8 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
                 newdict["snpDensity"] = newdict["snpCount"] = 0
 
             try:
-                newdict['GeneLength'] = 1000.0 * (newdict['TxEnd'] - newdict['TxStart'])
+                newdict['GeneLength'] = 1000.0 * \
+                    (newdict['TxEnd'] - newdict['TxStart'])
             except:
                 pass
 
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index f3b1b1fc..5bf8822a 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -591,7 +591,7 @@ class DisplayMappingResults:
         intCanvas = Image.new("RGBA", size=(self.graphWidth, self.graphHeight))
         with Bench("Drawing Plot"):
             gifmap = self.plotIntMapping(
-                intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm)
+                intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm=showLocusForm)
 
         self.gifmap = gifmap.__str__()
 
@@ -610,7 +610,7 @@ class DisplayMappingResults:
             intCanvasX2 = Image.new("RGBA", size=(
                 self.graphWidth * 2, self.graphHeight * 2))
             gifmapX2 = self.plotIntMapping(
-                intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm, zoom=2)
+                intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm=showLocusForm, zoom=2)
             intCanvasX2.save(
                 "{}.png".format(
                     os.path.join(webqtlConfig.GENERATED_IMAGE_DIR,
@@ -628,8 +628,8 @@ class DisplayMappingResults:
                 name=showLocusForm,
                 submit=HtmlGenWrapper.create_input_tag(type_='hidden'))
 
-            hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet+ \
-                    "Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
+            hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet + \
+                    "Geno", 'CellID': '_', 'RISet': fd.RISet, 'incparentsf1': 'ON'}
             for key in hddn.keys():
                 showLocusForm.append(HtmlGenWrapper.create_input_tag(
                     name=key, value=hddn[key], type_='hidden'))
@@ -651,7 +651,7 @@ class DisplayMappingResults:
             btminfo.append(
                 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
 
-    def plotIntMapping(self, canvas, offset=(80, 120, 90, 100), zoom=1, startMb= None, endMb = None, showLocusForm = ""):
+    def plotIntMapping(self, canvas, offset=(80, 120, 90, 100), zoom=1, startMb=None, endMb=None, showLocusForm=""):
         im_drawer = ImageDraw.Draw(canvas)
         # calculating margins
         xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -730,7 +730,7 @@ class DisplayMappingResults:
                                   zoom=zoom, startMb=startMb, endMb=endMb)
             if self.SNPChecked:
                 self.drawSNPTrackNew(
-                    canvas, offset=newoffset, zoom=2 * zoom, startMb=startMb, endMb = endMb)
+                    canvas, offset=newoffset, zoom=2 * zoom, startMb=startMb, endMb=endMb)
 # BEGIN HaplotypeAnalyst
             if self.haplotypeAnalystChecked:
                 self.drawHaplotypeBand(
@@ -758,7 +758,7 @@ class DisplayMappingResults:
 
         return gifmap
 
-    def drawBootStrapResult(self, canvas, nboot, drawAreaHeight, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+    def drawBootStrapResult(self, canvas, nboot, drawAreaHeight, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
         im_drawer = ImageDraw.Draw(canvas)
         xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
         plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
@@ -873,14 +873,14 @@ class DisplayMappingResults:
             font=VERDANA_FILE, size=13 * fontZoom)
         im_drawer.rectangle(
             xy=((canvas.size[0] - bootOffset, yZero - bootHeightThresh),
-                (canvas.size[0] - bootOffset - 15*zoom, yZero)),
+                (canvas.size[0] - bootOffset - 15 * zoom, yZero)),
             fill=YELLOW, outline=BLACK)
         im_drawer.line(
             xy=((canvas.size[0] - bootOffset + 4, yZero),
                 (canvas.size[0] - bootOffset, yZero)),
             fill=BLACK)
         TEXT_Y_DISPLACEMENT = -8
-        im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, yZero+TEXT_Y_DISPLACEMENT), text='0%',
+        im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, yZero + TEXT_Y_DISPLACEMENT), text='0%',
                        font=bootScaleFont, fill=BLACK)
 
         for item in bootScale:
@@ -891,7 +891,7 @@ class DisplayMappingResults:
                 xy=((canvas.size[0] - bootOffset + 4, bootY),
                     (canvas.size[0] - bootOffset, bootY)),
                 fill=BLACK)
-            im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, bootY+TEXT_Y_DISPLACEMENT),
+            im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, bootY + TEXT_Y_DISPLACEMENT),
                            text='%2.1f' % item, font=bootScaleFont, fill=BLACK)
 
         if self.legendChecked:
@@ -910,7 +910,7 @@ class DisplayMappingResults:
                            text='Frequency of the Peak LRS',
                            font=smallLabelFont, fill=BLACK)
 
-    def drawProbeSetPosition(self, canvas, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+    def drawProbeSetPosition(self, canvas, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
         im_drawer = ImageDraw.Draw(canvas)
         if len(self.traitList) != 1:
             return
@@ -987,7 +987,7 @@ class DisplayMappingResults:
             draw_open_polygon(canvas, xy=traitPixel, outline=BLACK,
                               fill=self.TRANSCRIPT_LOCATION_COLOR)
 
-    def drawSNPTrackNew(self, canvas, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+    def drawSNPTrackNew(self, canvas, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
         im_drawer = ImageDraw.Draw(canvas)
         if self.plotScale != 'physic' or self.selectedChr == -1 or not self.diffCol:
             return
@@ -1059,7 +1059,7 @@ class DisplayMappingResults:
 
             im_drawer.rectangle(
                 xy=((rightShift, yPaddingTop + kstep * 15),
-                    (rectWidth + rightShift, yPaddingTop + 10+kstep*15)),
+                    (rectWidth + rightShift, yPaddingTop + 10 + kstep * 15)),
                 fill=thisLRSColor, outline=BLACK)
             im_drawer.text(
                 text=name, xy=(rectWidth + 2 + rightShift,
@@ -1303,7 +1303,7 @@ class DisplayMappingResults:
                     text=string4, xy=(xLeftOffset, y_constant * fontZoom),
                     font=labelFont, fill=labelColor)
 
-    def drawGeneBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+    def drawGeneBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
         im_drawer = ImageDraw.Draw(canvas)
         if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
             return
@@ -1434,7 +1434,7 @@ class DisplayMappingResults:
                     xy=(
                         (geneStartPix, geneYLocation + \
                          self.EACH_GENE_HEIGHT / 2 * zoom),
-                        (geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 *zoom)),
+                        (geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 * zoom)),
                     fill=outlineColor, width=1)
 
                 # draw the arrows
@@ -1558,7 +1558,7 @@ class DisplayMappingResults:
                     target="_blank"))
 
 # BEGIN HaplotypeAnalyst
-    def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+    def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
         if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
             return
 
@@ -1630,7 +1630,7 @@ class DisplayMappingResults:
                     geneStartPix = xLeftOffset + plotXScale * \
                         (float(txStart) - startMb) - 0
                     geneEndPix = xLeftOffset + plotXScale * \
-                        (float(txEnd) - startMb)  + 0
+                        (float(txEnd) - startMb) + 0
 
                     if oldgeneEndPix >= xLeftOffset:
                         drawStart = oldgeneEndPix + 4
@@ -1707,19 +1707,19 @@ class DisplayMappingResults:
 
                                     im_drawer.line(
                                         xy=((drawStart,
-                                             geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
+                                             geneYLocation + 7 + 2 * ind * self.EACH_GENE_HEIGHT * zoom),
                                             (drawEnd,
-                                             geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)),
-                                        fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
+                                             geneYLocation + 7 + 2 * ind * self.EACH_GENE_HEIGHT * zoom)),
+                                        fill=mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
 
                                     fillColor = BLACK
                                     outlineColor = BLACK
                                     if lastGene == 0:
                                         im_drawer.rectangle(
                                             xy=((geneStartPix,
-                                                 geneYLocation + 2 * ind*self.EACH_GENE_HEIGHT*zoom),
+                                                 geneYLocation + 2 * ind * self.EACH_GENE_HEIGHT * zoom),
                                                 (geneEndPix,
-                                                 geneYLocation + 2 *ind*self.EACH_GENE_HEIGHT + 2*self.EACH_GENE_HEIGHT*zoom)),
+                                                 geneYLocation + 2 * ind * self.EACH_GENE_HEIGHT + 2 * self.EACH_GENE_HEIGHT * zoom)),
                                             outline=outlineColor, fill=fillColor)
 
                                     COORDS = "%d, %d, %d, %d" % (
@@ -1741,10 +1741,10 @@ class DisplayMappingResults:
                                         mylineColor = self.HAPLOTYPE_RECOMBINATION
                                     im_drawer.line(
                                         xy=((plotRight,
-                                             geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
+                                             geneYLocation + 7 + 2 * ind * self.EACH_GENE_HEIGHT * zoom),
                                             (drawEnd,
-                                             geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)),
-                                        fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
+                                             geneYLocation + 7 + 2 * ind * self.EACH_GENE_HEIGHT * zoom)),
+                                        fill=mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
 
                             if lastGene == 0:
                                 draw_rotated_text(
@@ -1752,7 +1752,7 @@ class DisplayMappingResults:
                                     font=ImageFont.truetype(font=VERDANA_FILE,
                                                             size=12),
                                     xy=(geneStartPix,
-                                        geneYLocation + 17 + 2*maxind*self.EACH_GENE_HEIGHT*zoom),
+                                        geneYLocation + 17 + 2 * maxind * self.EACH_GENE_HEIGHT * zoom),
                                     fill=BLACK, angle=-90)
 
                             oldgeneEndPix = geneEndPix
@@ -1778,21 +1778,21 @@ class DisplayMappingResults:
                         im_drawer.text(
                             text="%s" % (samplelist[j]),
                             xy=((xLeftOffset + plotWidth + 10),
-                                geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
+                                geneYLocation + 11 + 2 * ind * self.EACH_GENE_HEIGHT * zoom),
                             font=ImageFont.truetype(
                                 font=VERDANA_FILE, size=12),
                             fill=BLACK)
                         im_drawer.text(
                             text="%2.2f" % (expr),
                             xy=((xLeftOffset + plotWidth + 60),
-                                geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
+                                geneYLocation + 11 + 2 * ind * self.EACH_GENE_HEIGHT * zoom),
                             font=ImageFont.truetype(
                                 font=VERDANA_FILE, size=12),
                             fill=BLACK)
 
 # END HaplotypeAnalyst
 
-    def drawClickBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+    def drawClickBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
         im_drawer = ImageDraw.Draw(canvas)
         if self.plotScale != 'physic' or self.selectedChr == -1:
             return
@@ -1817,8 +1817,8 @@ class DisplayMappingResults:
 
         numBasesCurrentlyOnScreen = self.kONE_MILLION * \
             abs(startMb - endMb)  # Number of bases on screen now
-        flankingWidthInBases = int (
-            min((float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION)))
+        flankingWidthInBases = int(
+            min((float(numBasesCurrentlyOnScreen) / 2.0), (5 * self.kONE_MILLION)))
         webqtlZoomWidth = numBasesCurrentlyOnScreen / 16.0
         # Flanking width should be such that we either zoom in to a 10 million base region, or we show the clicked region at the same scale as we are currently seeing.
 
@@ -1990,7 +1990,7 @@ class DisplayMappingResults:
             # end of drawBrowserClickableRegions
         pass
 
-    def drawXAxis(self, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+    def drawXAxis(self, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
         im_drawer = ImageDraw.Draw(canvas)
         xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
         plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
@@ -2087,7 +2087,7 @@ class DisplayMappingResults:
                 xy=(
                     xLeftOffset + (plotWidth - im_drawer.textsize(
                         "Megabases", font=megabaseLabelFont)[0]) / 2,
-                    strYLoc + MBLabelFont.font.height + 10*(zoom%2)),
+                    strYLoc + MBLabelFont.font.height + 10 * (zoom % 2)),
                 font=megabaseLabelFont, fill=BLACK)
             pass
         else:
@@ -2110,7 +2110,7 @@ class DisplayMappingResults:
                                 thisChr.append(
                                     [_locus.name, _locus.cM - Locus0CM])
                     else:
-                        for j in (0, nLoci / 4, nLoci / 2, nLoci*3/4, -1):
+                        for j in (0, nLoci / 4, nLoci / 2, nLoci * 3 / 4, -1):
                             while _chr[j].name == ' - ':
                                 j += 1
                             if _chr[j].cM != preLpos:
@@ -2162,23 +2162,23 @@ class DisplayMappingResults:
                                                             yZero + 25)),
                             fill=lineColor)
                         im_drawer.line(
-                            xy=((xLeftOffset + offsetA, yZero + 25), (xLeftOffset+offsetA,\
-                                                                      yZero + 40 + Zorder*(LRectWidth+3))),
+                            xy=((xLeftOffset + offsetA, yZero + 25), (xLeftOffset + offsetA,\
+                                                                      yZero + 40 + Zorder * (LRectWidth + 3))),
                             fill=lineColor)
                         rectColor = ORANGE
                     else:
                         im_drawer.line(
-                            xy=((xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3)-3), (\
-                                xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3))),
+                            xy=((xLeftOffset + offsetA, yZero + 40 + Zorder * (LRectWidth + 3) - 3), (\
+                                xLeftOffset + offsetA, yZero + 40 + Zorder * (LRectWidth + 3))),
                             fill=lineColor)
                         rectColor = DEEPPINK
                     im_drawer.rectangle(
-                        xy=((xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3)),
+                        xy=((xLeftOffset + offsetA, yZero + 40 + Zorder * (LRectWidth + 3)),
                             (xLeftOffset + offsetA - LRectHeight,
-                             yZero + 40 + Zorder*(LRectWidth+3)+LRectWidth)),
+                             yZero + 40 + Zorder * (LRectWidth + 3) + LRectWidth)),
                         outline=rectColor, fill=rectColor, width=0)
-                    COORDS = "%d,%d,%d,%d" % (xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
-                                              xLeftOffset + offsetA, yZero +40+Zorder*(LRectWidth+3)+LRectWidth)
+                    COORDS = "%d,%d,%d,%d" % (xLeftOffset + offsetA - LRectHeight, yZero + 40 + Zorder * (LRectWidth + 3),\
+                                              xLeftOffset + offsetA, yZero + 40 + Zorder * (LRectWidth + 3) + LRectWidth)
                     HREF = "/show_trait?trait_id=%s&dataset=%s" % (
                         Lname, self.dataset.group.name + "Geno")
                     #HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
@@ -2203,13 +2203,13 @@ class DisplayMappingResults:
                 text="Centimorgans",
                 xy=(xLeftOffset + (plotWidth - im_drawer.textsize(
                     "Centimorgans", font=centimorganLabelFont)[0]) / 2,
-                    strYLoc + MBLabelFont.font.height + 10 * (zoom %2)),
+                    strYLoc + MBLabelFont.font.height + 10 * (zoom % 2)),
                 font=centimorganLabelFont, fill=BLACK)
 
         im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset + plotWidth, yZero)),
                        fill=BLACK, width=X_AXIS_THICKNESS)  # Draw the X axis itself
 
-    def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+    def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
         im_drawer = ImageDraw.Draw(canvas)
         xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
         plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
@@ -2364,7 +2364,7 @@ class DisplayMappingResults:
             TEXT_Y_DISPLACEMENT = -10
             im_drawer.text(
                 text=scaleStr,
-                xy=(xLeftOffset - 4 - im_drawer.textsize(scaleStr, font=LRSScaleFont)[0]-5,
+                xy=(xLeftOffset - 4 - im_drawer.textsize(scaleStr, font=LRSScaleFont)[0] - 5,
                     yLRS + TEXT_Y_DISPLACEMENT),
                 font=LRSScaleFont, fill=self.LRS_COLOR)
 
@@ -2479,7 +2479,7 @@ class DisplayMappingResults:
                         if k > 0:
                             Xc0, Yc0 = AdditiveCoordXY[k - 1]
                             Xc, Yc = aPoint
-                            if (Yc0 - yZero) * (Yc-yZero) < 0:
+                            if (Yc0 - yZero) * (Yc - yZero) < 0:
                                 if Xc == Xc0:  # genotype , locus distance is 0
                                     Xcm = Xc
                                 else:
@@ -2509,7 +2509,7 @@ class DisplayMappingResults:
                                         fill=plusColor, width=lineWidth
                                         # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
                                     )
-                            elif (Yc0 - yZero) * (Yc-yZero) > 0:
+                            elif (Yc0 - yZero) * (Yc - yZero) > 0:
                                 if Yc < yZero:
                                     im_drawer.line(
                                         xy=((Xc0, Yc0), (Xc, Yc)),
@@ -2660,7 +2660,7 @@ class DisplayMappingResults:
                 if k > 0:
                     Xc0, Yc0 = AdditiveCoordXY[k - 1]
                     Xc, Yc = aPoint
-                    if (Yc0 - yZero) * (Yc-yZero) < 0:
+                    if (Yc0 - yZero) * (Yc - yZero) < 0:
                         if Xc == Xc0:  # genotype , locus distance is 0
                             Xcm = Xc
                         else:
@@ -2689,7 +2689,7 @@ class DisplayMappingResults:
                                 fill=plusColor, width=lineWidth
                                 # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
                             )
-                    elif (Yc0 - yZero) * (Yc-yZero) > 0:
+                    elif (Yc0 - yZero) * (Yc - yZero) > 0:
                         if Yc < yZero:
                             im_drawer.line(
                                 xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor,
@@ -2726,7 +2726,7 @@ class DisplayMappingResults:
                 if k > 0:
                     Xc0, Yc0 = DominanceCoordXY[k - 1]
                     Xc, Yc = aPoint
-                    if (Yc0 - yZero) * (Yc-yZero) < 0:
+                    if (Yc0 - yZero) * (Yc - yZero) < 0:
                         if Xc == Xc0:  # genotype , locus distance is 0
                             Xcm = Xc
                         else:
@@ -2754,7 +2754,7 @@ class DisplayMappingResults:
                                 fill=plusColor, width=lineWidth
                                 # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
                             )
-                    elif (Yc0 - yZero) * (Yc-yZero) > 0:
+                    elif (Yc0 - yZero) * (Yc - yZero) > 0:
                         if Yc < yZero:
                             im_drawer.line(
                                 xy=((Xc0, Yc0), (Xc, Yc)),
@@ -2805,8 +2805,8 @@ class DisplayMappingResults:
                 scaleStr = "%2.3f" % item
                 im_drawer.text(
                     text=scaleStr,
-                    xy= (xLeftOffset + plotWidth + 6,
-                         additiveY + TEXT_Y_DISPLACEMENT),
+                    xy=(xLeftOffset + plotWidth + 6,
+                        additiveY + TEXT_Y_DISPLACEMENT),
                     font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE)
 
             im_drawer.line(
@@ -2818,7 +2818,7 @@ class DisplayMappingResults:
             xy=((xLeftOffset, yZero), (xLeftOffset, yTopOffset + 30 * (zoom - 1))),
             fill=self.LRS_COLOR, width=1 * zoom)  # the blue line running up the y axis
 
-    def drawGraphBackground(self, canvas, gifmap, offset=(80, 120, 80, 50), zoom=1, startMb= None, endMb = None):
+    def drawGraphBackground(self, canvas, gifmap, offset=(80, 120, 80, 50), zoom=1, startMb=None, endMb=None):
         # conditions
         # multiple Chromosome view
         # single Chromosome Physical
@@ -2953,10 +2953,10 @@ class DisplayMappingResults:
                                           "SNP Count",
                                           "SNP Density",
                                           "Avg Expr",
-                                               "Human Chr",
-                                               "Mb Start (hg19)",
-                                               "Literature Correlation",
-                                               "Gene Description"]
+                                          "Human Chr",
+                                          "Mb Start (hg19)",
+                                          "Literature Correlation",
+                                          "Gene Description"]
             else:
                 gene_table_header_list = ["",
                                           "Index",
@@ -3073,12 +3073,12 @@ class DisplayMappingResults:
                                         geneIdString,
                                         theGO["GeneSymbol"],
                                         target="_blank")
-                                    ),
+                                        ),
                                     str(HtmlGenWrapper.create_link_tag(
                                         mouseStartString,
                                         "{:.6f}".format(txStart),
                                         target="_blank")
-                                    ),
+                                        ),
                                     str(HtmlGenWrapper.create_link_tag(
                                         "javascript:rangeView('{}', {:f}, {:f})".format(
                                             str(chr_as_int),
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 289f1d5c..f88c5ac8 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -150,7 +150,7 @@ def gen_covariates_file(this_dataset, covariates, samples):
         if dataset_name == "Temp":
             temp_group = trait_name.split("_")[2]
             dataset_ob = create_dataset(
-                dataset_name="Temp", dataset_type="Temp", group_name = temp_group)
+                dataset_name="Temp", dataset_type="Temp", group_name=temp_group)
         else:
             dataset_ob = create_dataset(covariate.split(":")[1])
         trait_ob = create_trait(dataset=dataset_ob,
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 5d16abde..4d6715ba 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -2,7 +2,8 @@ import os
 import math
 import string
 import random
-import json, re
+import json
+import re
 
 from base import webqtlConfig
 from base.trait import GeneralTrait
@@ -28,7 +29,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
         output_filename = (f"{this_dataset.group.name}_GWA_"
                            + ''.join(random.choice(string.ascii_uppercase + string.digits)
                                      for _ in range(6))
-        )
+                           )
         bootstrap_filename = None
         permu_filename = None
 
@@ -37,7 +38,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
             bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_"
                                   + ''.join(random.choice(string.ascii_uppercase + string.digits)
                                             for _ in range(6))
-            )
+                                  )
 
             opt_list.append("-b")
             opt_list.append(f"--n_bootstrap {str(num_bootstrap)}")
@@ -47,7 +48,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
             permu_filename = ("{this_dataset.group.name}_PERM_"
                               + ''.join(random.choice(string.ascii_uppercase
                                                       + string.digits) for _ in range(6))
-            )
+                              )
             opt_list.append("-n " + str(num_perm))
             opt_list.append(
                 "--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt")
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index cf8cf514..1fa3dffe 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -110,7 +110,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
         if do_control == "true":
             logger.info("Using covariate")
             result_data_frame = scantwo(
-                cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method, n_cluster = 16)
+                cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method, n_cluster=16)
         else:
             logger.info("No covariates")
             result_data_frame = scantwo(
@@ -140,14 +140,14 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
                 cross_object, strata_ob = add_perm_strata(
                     cross_object, perm_strata_list)
                 if do_control == "true" or cofactors != "":
-                    perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(
-                        num_perm), perm_strata = strata_ob, model=model, method=method)
+                    perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm=int(
+                        num_perm), perm_strata=strata_ob, model=model, method=method)
                 else:
                     perm_data_frame = scanone(
-                        cross_object, pheno_col="the_pheno", n_perm=num_perm, perm_strata = strata_ob, model=model, method=method)
+                        cross_object, pheno_col="the_pheno", n_perm=num_perm, perm_strata=strata_ob, model=model, method=method)
             else:
                 if do_control == "true" or cofactors != "":
-                    perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(
+                    perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm=int(
                         num_perm), model=model, method=method)
                 else:
                     perm_data_frame = scanone(
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 81e0a03f..32ccec48 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -67,7 +67,8 @@ class RunMapping:
         if 'genofile' in start_vars:
             if start_vars['genofile'] != "":
                 self.genofile_string = start_vars['genofile']
-                self.dataset.group.genofile = self.genofile_string.split(":")[0]
+                self.dataset.group.genofile = self.genofile_string.split(":")[
+                    0]
                 genofile_samplelist = get_genofile_samplelist(self.dataset)
 
         all_samples_ordered = self.dataset.group.all_samples_ordered()
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 822900cc..a222b87c 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -36,7 +36,7 @@ class User(Base):
 
     # json detailing when they became a superuser, otherwise empty
     superuser = Column(Text)
-                       # if not superuser
+    # if not superuser
 
     logins = relationship("Login",
                           order_by="desc(Login.timestamp)",
@@ -47,7 +47,7 @@ class User(Base):
     user_collections = relationship("UserCollection",
                                     order_by="asc(UserCollection.name)",
                                     lazy='dynamic',
-                          )
+                                    )
 
     def display_num_collections(self):
         """
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 61f3b202..b28c1b04 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -116,7 +116,7 @@ def add_group_to_resource():
             group_id = request.form['selected_group']
             resource_info = get_resource_info(resource_id)
             default_privileges = resource_info['default_mask']
-            return render_template("admin/set_group_privileges.html", resource_id=resource_id, group_id=group_id, default_privileges = default_privileges)
+            return render_template("admin/set_group_privileges.html", resource_id=resource_id, group_id=group_id, default_privileges=default_privileges)
         elif all(key in request.form for key in ('data_privilege', 'metadata_privilege', 'admin_privilege')):
             group_id = request.form['group_id']
             group_name = get_group_info(group_id)['name']
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index fc48959e..3cbda3dd 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -276,7 +276,7 @@ class SearchResultPage:
                                       search_operator,
                                       self.dataset,
                                       search_type['key']
-                                    )
+                                      )
             return the_search
         else:
             return None
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 42fe339e..c4d0e135 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -28,10 +28,10 @@ class SnpBrowser:
 
             if self.limit_strains == "true":
                 self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(
-                    variant_type=self.variant_type, strains=self.chosen_strains, empty_columns = self.empty_columns)
+                    variant_type=self.variant_type, strains=self.chosen_strains, empty_columns=self.empty_columns)
             else:
                 self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(
-                    variant_type=self.variant_type, strains=self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
+                    variant_type=self.variant_type, strains=self.strain_lists, species=self.species_name, empty_columns=self.empty_columns)
 
     def initialize_parameters(self, start_vars):
         if 'first_run' in start_vars:
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 0d5f1f3e..ff77982f 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -65,7 +65,7 @@ def set_password(password):
         "salt": base64.b64encode(os.urandom(32)),
         "iterations": 100000,
         "keylength": 32,
-      "created_timestamp": timestamp()
+        "created_timestamp": timestamp()
     }
 
     assert len(password) >= 6, "Password shouldn't be shorter than 6 characters"
@@ -132,7 +132,7 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
     logger.info("Successfully sent email to " + toaddr)
 
 
-def send_verification_email(user_details, template_name="email/user_verification.txt", key_prefix="verification_code", subject = "GeneNetwork e-mail verification"):
+def send_verification_email(user_details, template_name="email/user_verification.txt", key_prefix="verification_code", subject="GeneNetwork e-mail verification"):
     verification_code = str(uuid.uuid4())
     key = key_prefix + ":" + verification_code
 
@@ -147,7 +147,7 @@ def send_verification_email(user_details, template_name="email/user_verification
     return {"recipient": recipient, "subject": subject, "body": body}
 
 
-def send_invitation_email(user_email, temp_password, template_name="email/user_invitation.txt", subject= "You've been added to a GeneNetwork user group"):
+def send_invitation_email(user_email, temp_password, template_name="email/user_invitation.txt", subject="You've been added to a GeneNetwork user group"):
     recipient = user_email
     body = render_template(template_name, temp_password)
     send_email(recipient, subject, body)
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index fb26bfb1..cf84ea73 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -476,7 +476,7 @@ def set_password(password, user):
 
     user.password = json.dumps(pwfields.__dict__,
                                sort_keys=True,
-                                   )
+                               )
 
 
 class VerificationEmail:
@@ -677,7 +677,7 @@ def github_oauth2():
     user_details = get_user_by_unique_column("github_id", github_user["id"])
     if user_details == None:
         user_details = {
-            "user_id": str(uuid.uuid4()), "name": github_user["name"].encode("utf-8"), "github_id": github_user["id"], "user_url": github_user["html_url"].encode("utf-8")            , "login_type": "github"            , "organization": ""            , "active": 1            , "confirmed": 1
+            "user_id": str(uuid.uuid4()), "name": github_user["name"].encode("utf-8"), "github_id": github_user["id"], "user_url": github_user["html_url"].encode("utf-8"), "login_type": "github", "organization": "", "active": 1, "confirmed": 1
         }
         save_user(user_details, user_details["user_id"])
 
@@ -705,7 +705,7 @@ def orcid_oauth2():
             user_details = {
                 "user_id": str(uuid4()), "name": result_dict["name"], "orcid": result_dict["orcid"], "user_url": "%s/%s" % (
                     "/".join(ORCID_AUTH_URL.split("/")[:-2]),
-                    result_dict["orcid"]), "login_type": "orcid", "organization": "", "active": 1                , "confirmed": 1
+                    result_dict["orcid"]), "login_type": "orcid", "organization": "", "active": 1, "confirmed": 1
             }
             save_user(user_details, user_details["user_id"])
 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index f75209ff..f9b8f310 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -141,7 +141,7 @@ def handle_bad_request(e):
     now = datetime.datetime.utcnow()
     time_str = now.strftime('%l:%M%p UTC %b %d, %Y')
     formatted_lines = [request.url
-                       + " (" + time_str + ")"]+traceback.format_exc().splitlines()
+                       + " (" + time_str + ")"] + traceback.format_exc().splitlines()
 
     # Handle random animations
     # Use a cookie to have one animation on refresh