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-rw-r--r--wqflask/base/GeneralObject.py4
-rw-r--r--wqflask/base/data_set.py4
-rw-r--r--wqflask/base/trait.py10
-rw-r--r--wqflask/maintenance/generate_probesetfreeze_file.py7
-rw-r--r--wqflask/tests/unit/base/test_data_set.py10
-rw-r--r--wqflask/tests/unit/wqflask/api/test_gen_menu.py68
-rw-r--r--wqflask/utility/svg.py24
-rw-r--r--wqflask/wqflask/api/gen_menu.py10
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py10
-rw-r--r--wqflask/wqflask/db_info.py34
-rw-r--r--wqflask/wqflask/do_search.py12
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py14
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py4
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py4
-rw-r--r--wqflask/wqflask/user_session.py4
-rw-r--r--wqflask/wqflask/views.py12
16 files changed, 116 insertions, 115 deletions
diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py
index 249195e2..ce8e60b8 100644
--- a/wqflask/base/GeneralObject.py
+++ b/wqflask/base/GeneralObject.py
@@ -62,5 +62,5 @@ class GeneralObject:
return s
def __eq__(self, other):
- return (len(list(self.__dict__.keys())) ==
- len(list(other.__dict__.keys())))
+ return (len(list(self.__dict__.keys()))
+ == len(list(other.__dict__.keys())))
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 8ec0aaad..5eac695e 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1032,8 +1032,8 @@ class MrnaAssayDataSet(DataSet):
else:
description_display = this_trait.symbol
- if (len(description_display) > 1 and description_display != 'N/A' and
- len(target_string) > 1 and target_string != 'None'):
+ if (len(description_display) > 1 and description_display != 'N/A'
+ and len(target_string) > 1 and target_string != 'None'):
description_display = description_display + '; ' + target_string.strip()
# Save it for the jinja2 template
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 5574128d..d09cfd40 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -479,9 +479,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
else:
description_display = trait.symbol
- if (str(description_display or "") != "" and
- description_display != 'N/A' and
- str(target_string or "") != "" and target_string != 'None'):
+ if (str(description_display or "") != ""
+ and description_display != 'N/A'
+ and str(target_string or "") != "" and target_string != 'None'):
description_display = description_display + '; ' + target_string.strip()
# Save it for the jinja2 template
@@ -575,6 +575,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if str(trait.lrs or "") != "":
trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
else:
- raise KeyError(repr(trait.name) +
- ' information is not found in the database.')
+ raise KeyError(repr(trait.name)
+ + ' information is not found in the database.')
return trait
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
index bd9c2ab4..e964c8ed 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -110,9 +110,10 @@ def write_data_matrix_file(strains, probeset_vals, filename):
def main():
- filename = os.path.expanduser("~/gene/wqflask/maintenance/" +
- "ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2" +
- "(Oct08)_RankInv_Beta.txt")
+ filename = os.path.expanduser(
+ "~/gene/wqflask/maintenance/"
+ "ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2"
+ "(Oct08)_RankInv_Beta.txt")
dataset_name = "Eye_AXBXA_1008_RankInv"
cursor = get_cursor()
diff --git a/wqflask/tests/unit/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py
index ee5d6f06..66ad361d 100644
--- a/wqflask/tests/unit/base/test_data_set.py
+++ b/wqflask/tests/unit/base/test_data_set.py
@@ -88,8 +88,8 @@ class TestDataSetTypes(unittest.TestCase):
'"B139_K_1206_R": "ProbeSet", '
'"Test": "ProbeSet"}'))
db_mock.db.execute.assert_called_once_with(
- ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze " +
- "WHERE ProbeSetFreeze.Name = \"Test\" ")
+ ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze "
+ + "WHERE ProbeSetFreeze.Name = \"Test\" ")
)
@mock.patch('base.data_set.g')
@@ -145,9 +145,9 @@ class TestDataSetTypes(unittest.TestCase):
'"Test": "Publish"}'))
db_mock.db.execute.assert_called_with(
- ("SELECT PublishFreeze.Name " +
- "FROM PublishFreeze, InbredSet " +
- "WHERE InbredSet.Name = 'Test' AND "
+ ("SELECT PublishFreeze.Name "
+ + "FROM PublishFreeze, InbredSet "
+ + "WHERE InbredSet.Name = 'Test' AND "
"PublishFreeze.InbredSetId = InbredSet.Id")
)
diff --git a/wqflask/tests/unit/wqflask/api/test_gen_menu.py b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
index 57eb1650..fd0fe52e 100644
--- a/wqflask/tests/unit/wqflask/api/test_gen_menu.py
+++ b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
@@ -105,13 +105,13 @@ class TestGenMenu(unittest.TestCase):
for name in ["mouse", "human"]:
db_mock.db.execute.assert_any_call(
("SELECT InbredSet.Name, InbredSet.FullName, " +
- "IFNULL(InbredSet.Family, 'None') " +
- "FROM InbredSet, Species WHERE Species.Name " +
- "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by " +
- "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, " +
- "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, " +
- "InbredSet.FullName) ASC, InbredSet.FullName ASC, " +
- "InbredSet.MenuOrderId ASC").format(name)
+ "IFNULL(InbredSet.Family, 'None') "
+ + "FROM InbredSet, Species WHERE Species.Name "
+ + "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by "
+ + "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, "
+ + "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, "
+ + "InbredSet.FullName) ASC, InbredSet.FullName ASC, "
+ + "InbredSet.MenuOrderId ASC").format(name)
)
@mock.patch('wqflask.api.gen_menu.g')
@@ -172,12 +172,12 @@ class TestGenMenu(unittest.TestCase):
self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"),
[['602', "BXDPublish", "BXD Published Phenotypes"]])
db_mock.db.execute.assert_called_with(
- "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, " +
- "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, " +
- "InbredSet WHERE InbredSet.Name = 'BXD' AND " +
- "PublishFreeze.InbredSetId = InbredSet.Id AND " +
- "InfoFiles.InfoPageName = PublishFreeze.Name " +
- "ORDER BY PublishFreeze.CreateTime ASC"
+ "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, "
+ + "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, "
+ + "InbredSet WHERE InbredSet.Name = 'BXD' AND "
+ + "PublishFreeze.InbredSetId = InbredSet.Id AND "
+ + "InfoFiles.InfoPageName = PublishFreeze.Name "
+ + "ORDER BY PublishFreeze.CreateTime ASC"
)
self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"),
[['602', "BXDPublish", "Mouse Phenome Database"]])
@@ -221,8 +221,8 @@ class TestGenMenu(unittest.TestCase):
"SELECT InfoFiles.GN_AccesionId FROM InfoFiles, "
"GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND "
"GenoFreeze.InbredSetId = InbredSet.Id AND "
- "InfoFiles.InfoPageName = GenoFreeze.ShortName " +
- "ORDER BY GenoFreeze.CreateTime DESC"
+ "InfoFiles.InfoPageName = GenoFreeze.ShortName "
+ + "ORDER BY GenoFreeze.CreateTime DESC"
)
db_mock.db.execute.return_value.fetchone.return_value = ()
self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"),
@@ -239,16 +239,16 @@ class TestGenMenu(unittest.TestCase):
"112", 'HC_M2_0606_P', "Hippocampus Consortium M430v2 (Jun06) PDNN"
]])
db_mock.db.execute.assert_called_once_with(
- "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, " +
- "ProbeSetFreeze.FullName FROM ProbeSetFreeze, " +
- "ProbeFreeze, InbredSet, Tissue, Species WHERE " +
- "Species.Name = 'Mouse' AND Species.Id = " +
- "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND " +
- "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND " +
- "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = " +
- "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND " +
- "ProbeSetFreeze.public > 0 " +
- "ORDER BY -ProbeSetFreeze.OrderList DESC, ProbeSetFreeze.CreateTime DESC")
+ "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, "
+ + "ProbeSetFreeze.FullName FROM ProbeSetFreeze, "
+ + "ProbeFreeze, InbredSet, Tissue, Species WHERE "
+ + "Species.Name = 'Mouse' AND Species.Id = "
+ + "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND "
+ + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND "
+ + "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = "
+ + "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND "
+ + "ProbeSetFreeze.public > 0 "
+ + "ORDER BY -ProbeSetFreeze.OrderList DESC, ProbeSetFreeze.CreateTime DESC")
@mock.patch('wqflask.api.gen_menu.build_datasets')
@mock.patch('wqflask.api.gen_menu.g')
@@ -266,15 +266,15 @@ class TestGenMenu(unittest.TestCase):
['H', 'H', 'Molecular Traits'],
['R', 'R', 'Molecular Traits']])
db_mock.db.execute.assert_called_once_with(
- "SELECT DISTINCT Tissue.Name " +
- "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, " +
- "Tissue, Species WHERE Species.Name = 'mouse' " +
- "AND Species.Id = InbredSet.SpeciesId AND " +
- "InbredSet.Name = 'random group' AND " +
- "ProbeFreeze.TissueId = Tissue.Id AND " +
- "ProbeFreeze.InbredSetId = InbredSet.Id AND " +
- "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " +
- "ORDER BY Tissue.Name"
+ "SELECT DISTINCT Tissue.Name "
+ + "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, "
+ + "Tissue, Species WHERE Species.Name = 'mouse' "
+ + "AND Species.Id = InbredSet.SpeciesId AND "
+ + "InbredSet.Name = 'random group' AND "
+ + "ProbeFreeze.TissueId = Tissue.Id AND "
+ + "ProbeFreeze.InbredSetId = InbredSet.Id AND "
+ + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+ + "ORDER BY Tissue.Name"
)
@mock.patch('wqflask.api.gen_menu.build_types')
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 8d2e13ab..bc3bc833 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)
@@ -319,11 +319,11 @@ class SVGelement:
f.write('\t' * level)
f.write('<' + self.type)
for attkey in list(self.attributes.keys()):
- f.write(' ' + _escape(str(attkey)) + '=' +
- _quoteattr(str(self.attributes[attkey])))
+ f.write(' ' + _escape(str(attkey)) + '='
+ + _quoteattr(str(self.attributes[attkey])))
if self.namespace:
- f.write(' xmlns="' + _escape(str(self.namespace)) +
- '" xmlns:xlink="http://www.w3.org/1999/xlink"')
+ f.write(' xmlns="' + _escape(str(self.namespace))
+ + '" xmlns:xlink="http://www.w3.org/1999/xlink"')
if self.elements or self.text or self.cdata:
f.write('>')
if self.elements:
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index a64524dd..e65b36e4 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -179,11 +179,11 @@ def build_datasets(species, group, type_name):
elif type_name == "Genotypes":
results = g.db.execute(
("SELECT InfoFiles.GN_AccesionId " +
- "FROM InfoFiles, GenoFreeze, InbredSet " +
- "WHERE InbredSet.Name = '{}' AND " +
- "GenoFreeze.InbredSetId = InbredSet.Id AND " +
- "InfoFiles.InfoPageName = GenoFreeze.ShortName " +
- "ORDER BY GenoFreeze.CreateTime DESC").format(group)).fetchone()
+ "FROM InfoFiles, GenoFreeze, InbredSet "
+ + "WHERE InbredSet.Name = '{}' AND "
+ + "GenoFreeze.InbredSetId = InbredSet.Id AND "
+ + "InfoFiles.InfoPageName = GenoFreeze.ShortName "
+ + "ORDER BY GenoFreeze.CreateTime DESC").format(group)).fetchone()
dataset_id = "None"
if bool(results):
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 8ee24246..e8b7b057 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -96,9 +96,9 @@ class CorrelationResults:
self.p_range_lower = get_float(start_vars, 'p_range_lower', -1.0)
self.p_range_upper = get_float(start_vars, 'p_range_upper', 1.0)
- if ('loc_chr' in start_vars and
- 'min_loc_mb' in start_vars and
- 'max_loc_mb' in start_vars):
+ if ('loc_chr' in start_vars
+ and 'min_loc_mb' in start_vars
+ and 'max_loc_mb' in start_vars):
self.location_type = get_string(start_vars, 'location_type')
self.location_chr = get_string(start_vars, 'loc_chr')
@@ -200,8 +200,8 @@ class CorrelationResults:
if chr_info.name == trait_object.chr:
chr_as_int = order_id
- if (float(self.correlation_data[trait][0]) >= self.p_range_lower and
- float(self.correlation_data[trait][0]) <= self.p_range_upper):
+ if (float(self.correlation_data[trait][0]) >= self.p_range_lower
+ and float(self.correlation_data[trait][0]) <= self.p_range_upper):
if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean):
if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr):
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index 8d28fef0..938c453e 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -23,23 +23,23 @@ class InfoPage:
def get_info(self, create=False):
query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " +
- "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " +
- "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " +
- "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " +
- "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " +
- "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " +
- "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " +
- "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " +
- "FROM InfoFiles " +
- "LEFT JOIN Species USING (SpeciesId) " +
- "LEFT JOIN Tissue USING (TissueId) " +
- "LEFT JOIN InbredSet USING (InbredSetId) " +
- "LEFT JOIN GeneChip USING (GeneChipId) " +
- "LEFT JOIN AvgMethod USING (AvgMethodId) " +
- "LEFT JOIN Datasets USING (DatasetId) " +
- "LEFT JOIN Investigators USING (InvestigatorId) " +
- "LEFT JOIN Organizations USING (OrganizationId) " +
- "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ")
+ "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, "
+ + "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, "
+ + "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, "
+ + "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, "
+ + "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, "
+ + "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, "
+ + "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics "
+ + "FROM InfoFiles "
+ + "LEFT JOIN Species USING (SpeciesId) "
+ + "LEFT JOIN Tissue USING (TissueId) "
+ + "LEFT JOIN InbredSet USING (InbredSetId) "
+ + "LEFT JOIN GeneChip USING (GeneChipId) "
+ + "LEFT JOIN AvgMethod USING (AvgMethodId) "
+ + "LEFT JOIN Datasets USING (DatasetId) "
+ + "LEFT JOIN Investigators USING (InvestigatorId) "
+ + "LEFT JOIN Organizations USING (OrganizationId) "
+ + "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ")
if self.gn_accession_id:
final_query = query_base + \
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index e50ff50b..48527785 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -111,8 +111,8 @@ class MrnaAssaySearch(DoSearch):
else:
match_clause = ""
- where_clause = (match_clause +
- """ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ where_clause = (match_clause
+ + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
and ProbeSetXRef.ProbeSetFreezeId = %s
""" % (escape(str(self.dataset.id))))
@@ -134,8 +134,8 @@ class MrnaAssaySearch(DoSearch):
else:
match_clause = ""
- where_clause = (match_clause +
- """ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ where_clause = (match_clause
+ + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
and ProbeSetXRef.ProbeSetFreezeId = %s
""" % (escape(str(self.dataset.id))))
@@ -348,8 +348,8 @@ class GenotypeSearch(DoSearch):
from_clause = self.normalize_spaces(from_clause)
if self.search_term[0] == "*":
- query = (self.base_query +
- """WHERE Geno.Id = GenoXRef.GenoId
+ query = (self.base_query
+ + """WHERE Geno.Id = GenoXRef.GenoId
and GenoXRef.GenoFreezeId = GenoFreeze.Id
and GenoFreeze.Id = %s""" % (escape(str(self.dataset.id))))
else:
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index c51b7a9a..9f9591ad 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -25,8 +25,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
trait_filename = f"{str(this_trait.name)}_{str(this_dataset.name)}_pheno"
gen_pheno_txt_file(samples, vals, trait_filename)
- output_filename = (f"{this_dataset.group.name}_GWA_" +
- ''.join(random.choice(string.ascii_uppercase + string.digits)
+ output_filename = (f"{this_dataset.group.name}_GWA_"
+ + ''.join(random.choice(string.ascii_uppercase + string.digits)
for _ in range(6))
)
bootstrap_filename = None
@@ -34,8 +34,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
opt_list = []
if boot_check and num_bootstrap > 0:
- bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_" +
- ''.join(random.choice(string.ascii_uppercase + string.digits)
+ bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_"
+ + ''.join(random.choice(string.ascii_uppercase + string.digits)
for _ in range(6))
)
@@ -44,9 +44,9 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
opt_list.append(
f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt")
if num_perm > 0:
- permu_filename = ("{this_dataset.group.name}_PERM_" +
- ''.join(random.choice(string.ascii_uppercase +
- string.digits) for _ in range(6))
+ 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(
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 6419335e..3a63c84e 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -57,8 +57,8 @@ class SampleList:
sample = webqtlCaseData.webqtlCaseData(name=sample_name)
sample.extra_info = {}
- if (self.dataset.group.name == 'AXBXA' and
- sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17')):
+ if (self.dataset.group.name == 'AXBXA'
+ and sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17')):
sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
sample.extra_info['css_class'] = "fs12"
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 18cadea4..fcebbc4d 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -452,8 +452,8 @@ class ShowTrait:
for sample in list(self.this_trait.data.keys()):
if (self.this_trait.data[sample].name2 != self.this_trait.data[sample].name):
- if ((self.this_trait.data[sample].name2 in primary_sample_names) and
- (self.this_trait.data[sample].name not in primary_sample_names)):
+ if ((self.this_trait.data[sample].name2 in primary_sample_names)
+ and (self.this_trait.data[sample].name not in primary_sample_names)):
primary_sample_names.append(
self.this_trait.data[sample].name)
primary_sample_names.remove(
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 963288b3..3e543445 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -184,8 +184,8 @@ class UserSession:
# ZS: Get user's collections if they exist
collections = get_user_collections(self.user_id)
collections = [item for item in collections if item['name'] != "Your Default Collection"] + \
- [item for item in collections if item['name'] ==
- "Your Default Collection"] # ZS: Ensure Default Collection is last in list
+ [item for item in collections if item['name']
+ == "Your Default Collection"] # ZS: Ensure Default Collection is last in list
return collections
@property
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 2c53012a..f75209ff 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -140,8 +140,8 @@ def handle_bad_request(e):
logger.error(traceback.format_exc())
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()
+ formatted_lines = [request.url
+ + " (" + time_str + ")"]+traceback.format_exc().splitlines()
# Handle random animations
# Use a cookie to have one animation on refresh
@@ -518,10 +518,10 @@ def export_perm_data():
["#N_genotypes: " + str(perm_info['n_genotypes'])],
["#Genotype_file: " + perm_info['genofile']],
["#Units_linkage: " + perm_info['units_linkage']],
- ["#Permutation_stratified_by: " +
- ", ".join([str(cofactor) for cofactor in perm_info['strat_cofactors']])],
- ["#RESULTS_1: Suggestive LRS(p=0.63) = " +
- str(np.percentile(np.array(perm_info['perm_data']), 67))],
+ ["#Permutation_stratified_by: "
+ + ", ".join([str(cofactor) for cofactor in perm_info['strat_cofactors']])],
+ ["#RESULTS_1: Suggestive LRS(p=0.63) = "
+ + str(np.percentile(np.array(perm_info['perm_data']), 67))],
["#RESULTS_2: Significant LRS(p=0.05) = " + str(
np.percentile(np.array(perm_info['perm_data']), 95))],
["#RESULTS_3: Highly Significant LRS(p=0.01) = " + str(
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 07:49:50 +0000