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-rw-r--r--wqflask/base/webqtlConfig.py2
-rw-r--r--wqflask/maintenance/quantile_normalize.py2
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py7
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py4
-rw-r--r--wqflask/utility/Plot.py5
-rw-r--r--wqflask/utility/elasticsearch_tools.py2
-rw-r--r--wqflask/utility/svg.py50
-rw-r--r--wqflask/wqflask/api/mapping.py3
-rw-r--r--wqflask/wqflask/api/router.py30
-rw-r--r--wqflask/wqflask/collect.py8
-rw-r--r--wqflask/wqflask/correlation/corr_scatter_plot.py4
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py34
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py2
-rw-r--r--wqflask/wqflask/ctl/ctl_analysis.py2
-rw-r--r--wqflask/wqflask/group_manager.py8
-rw-r--r--wqflask/wqflask/interval_analyst/GeneUtil.py3
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py120
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py2
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py9
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py10
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py3
-rw-r--r--wqflask/wqflask/model.py4
-rw-r--r--wqflask/wqflask/resource_manager.py2
-rw-r--r--wqflask/wqflask/search_results.py2
-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py4
-rw-r--r--wqflask/wqflask/user_login.py6
-rw-r--r--wqflask/wqflask/user_manager.py6
-rw-r--r--wqflask/wqflask/views.py2
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