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authorBonfaceKilz2021-04-30 12:52:55 +0300
committerBonfaceKilz2021-04-30 13:45:15 +0300
commitbd702e59d7a426fe351d34367bf824683c655696 (patch)
tree95994298c5dc29e527a0646cd99a248c7bbd8a66
parentd1bc52a0d8e1219f377e804c3f27a3543d234fcb (diff)
downloadgenenetwork2-bd702e59d7a426fe351d34367bf824683c655696.tar.gz
autopep8: Fix W291, W292, W293, W391
-rw-r--r--wqflask/base/mrna_assay_tissue_data.py2
-rw-r--r--wqflask/maintenance/convert_dryad_to_bimbam.py2
-rw-r--r--wqflask/maintenance/convert_geno_to_bimbam.py4
-rw-r--r--wqflask/maintenance/generate_kinship_from_bimbam.py8
-rw-r--r--wqflask/maintenance/geno_to_json.py34
-rw-r--r--wqflask/tests/unit/wqflask/api/test_correlation.py4
-rw-r--r--wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py2
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py4
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py7
-rw-r--r--wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py8
-rw-r--r--wqflask/tests/unit/wqflask/test_server_side.py4
-rw-r--r--wqflask/utility/__init__.py2
-rw-r--r--wqflask/utility/genofile_parser.py1
-rw-r--r--wqflask/wqflask/__init__.py2
-rw-r--r--wqflask/wqflask/api/mapping.py2
-rw-r--r--wqflask/wqflask/api/router.py14
-rw-r--r--wqflask/wqflask/collect.py1
-rw-r--r--wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py7
-rw-r--r--wqflask/wqflask/correlation/corr_scatter_plot.py4
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py1
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py2
-rw-r--r--wqflask/wqflask/ctl/ctl_analysis.py3
-rw-r--r--wqflask/wqflask/db_info.py2
-rw-r--r--wqflask/wqflask/docs.py2
-rw-r--r--wqflask/wqflask/export_traits.py4
-rw-r--r--wqflask/wqflask/external_tools/send_to_webgestalt.py2
-rw-r--r--wqflask/wqflask/heatmap/heatmap.py2
-rw-r--r--wqflask/wqflask/interval_analyst/GeneUtil.py24
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py10
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py2
-rw-r--r--wqflask/wqflask/resource_manager.py2
-rw-r--r--wqflask/wqflask/search_results.py1
-rw-r--r--wqflask/wqflask/server_side.py2
-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py7
-rw-r--r--wqflask/wqflask/user_login.py42
-rw-r--r--wqflask/wqflask/user_session.py2
36 files changed, 98 insertions, 124 deletions
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 9bb29664..882ae911 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -74,7 +74,7 @@ class MrnaAssayTissueData:
def get_symbol_values_pairs(self):
id_list = [self.data[symbol].data_id for symbol in self.data]
-
+
symbol_values_dict = {}
if len(id_list) > 0:
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
index e417c280..18fbb8a1 100644
--- a/wqflask/maintenance/convert_dryad_to_bimbam.py
+++ b/wqflask/maintenance/convert_dryad_to_bimbam.py
@@ -52,7 +52,7 @@ def read_dryad_file(filename):
# this_row.append(line.split(" ")[i+2])
# print("row: " + str(i))
# geno_rows.append(this_row)
- #
+ #
# return geno_rows
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index a2ede1f9..c5af1ca6 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -91,7 +91,7 @@ class ConvertGenoFile:
self.markers.append(this_marker.__dict__)
- self.write_to_bimbam()
+ self.write_to_bimbam()
def write_to_bimbam(self):
with open(self.output_files[0], "w") as geno_fh:
@@ -126,7 +126,7 @@ class ConvertGenoFile:
self.sample_list = row_contents[3:]
else:
self.sample_list = row_contents[2:]
-
+
def process_rows(self):
for self.latest_row_pos, row in enumerate(self.input_fh):
self.latest_row_value = row
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index bed634fa..cd39fceb 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -19,7 +19,7 @@ class GenerateKinshipMatrices:
self.group_name = group_name
self.geno_file = geno_file
self.pheno_file = pheno_file
-
+
def generate_kinship(self):
gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + \
" -p " + self.pheno_file + \
@@ -56,11 +56,11 @@ class GenerateKinshipMatrices:
print(" Column is:", convertob.latest_col_value)
print(" Row is:", convertob.latest_row_value)
break
-
-
+
+
if __name__ == "__main__":
Geno_Directory = """/export/local/home/zas1024/genotype_files/genotype/"""
Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/"""
GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory)
-
+
# ./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index 76a0fc98..27eb6553 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -29,7 +29,7 @@ from pprint import pformat as pf
class EmptyConfigurations(Exception):
pass
-
+
class Marker:
def __init__(self):
self.name = None
@@ -42,20 +42,20 @@ class Marker:
class ConvertGenoFile:
def __init__(self, input_file, output_file):
-
+
self.input_file = input_file
self.output_file = output_file
-
+
self.mb_exists = False
self.cm_exists = False
self.markers = []
-
+
self.latest_row_pos = None
self.latest_col_pos = None
-
+
self.latest_row_value = None
self.latest_col_value = None
-
+
def convert(self):
self.haplotype_notation = {
@@ -64,16 +64,16 @@ class ConvertGenoFile:
'@het': "0.5",
'@unk': "NA"
}
-
+
self.configurations = {}
#self.skipped_cols = 3
-
+
# if self.input_file.endswith(".geno.gz"):
# print("self.input_file: ", self.input_file)
# self.input_fh = gzip.open(self.input_file)
# else:
self.input_fh = open(self.input_file)
-
+
with open(self.output_file, "w") as self.output_fh:
# if self.file_type == "geno":
self.process_csv()
@@ -105,22 +105,22 @@ class ConvertGenoFile:
self.configurations[genotype.upper()])
else:
this_marker.genotypes.append("NA")
-
- #print("this_marker is:", pf(this_marker.__dict__))
+
+ #print("this_marker is:", pf(this_marker.__dict__))
# if this_marker.chr == "14":
self.markers.append(this_marker.__dict__)
with open(self.output_file, 'w') as fh:
json.dump(self.markers, fh, indent=" ", sort_keys=True)
-
+
# print('configurations:', str(configurations))
#self.latest_col_pos = item_count + self.skipped_cols
#self.latest_col_value = item
-
+
# if item_count != 0:
# self.output_fh.write(" ")
# self.output_fh.write(self.configurations[item.upper()])
-
+
# self.output_fh.write("\n")
def process_rows(self):
@@ -176,12 +176,12 @@ class ConvertGenoFile:
print(" Column is:", convertob.latest_col_value)
print(" Row is:", convertob.latest_row_value)
break
-
+
# def process_snps_file(cls, snps_file, new_directory):
# output_file = os.path.join(new_directory, "mouse_families.json")
# print("%s -> %s" % (snps_file, output_file))
# convertob = ConvertGenoFile(input_file, output_file)
-
+
if __name__ == "__main__":
Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
@@ -192,5 +192,5 @@ if __name__ == "__main__":
# convertob.convert()
ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
# ConvertGenoFiles(Geno_Directory)
-
+
#process_csv(Input_File, Output_File)
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index bd99838d..34ffa9ef 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -105,9 +105,9 @@ class TestCorrelations(unittest.TestCase):
target_dataset = AttributeSetter({"group": group})
target_vals = [3.4, 6.2, 4.1, 3.4, 1.2, 5.6]
- trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}),
+ trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}),
"S3": AttributeSetter(
- {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}),
+ {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}),
"S6": AttributeSetter({"value": 5.0})}
this_trait = AttributeSetter({"data": trait_data})
mock_normalize.return_value = ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
index 44d2e0fc..2bbeab1f 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -5,7 +5,7 @@ from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_ti
class TestCorrelationFunctions(unittest.TestCase):
-
+
@mock.patch("wqflask.correlation.correlation_functions.MrnaAssayTissueData")
def test_get_trait_symbol_and_tissue_values(self, mock_class):
"""test for getting trait symbol and tissue_values"""
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 c762982b..1198740d 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -8,7 +8,7 @@ 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):
+ def test_gen_pheno_txt_file(self):
vals = ["V1", "x", "V4", "V3","x"]
samples = ["S1", "S2", "S3", "S4","S5"]
trait_filename = "trait_file"
@@ -21,5 +21,3 @@ class TestQtlReaperMapping(unittest.TestCase):
'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
filehandler.write.assert_has_calls(write_calls)
-
-
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 6996c275..d69a20d3 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -40,10 +40,3 @@ class TestRqtlMapping(unittest.TestCase):
expected_sanitized_name = "c('f',NA,'r',NA,NA)"
results = sanitize_rqtl_names(vals)
self.assertEqual(expected_sanitized_name, results)
-
-
-
-
-
-
-
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
index ce3e7b83..8823e1fc 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -21,9 +21,9 @@ class TestSnpBrowser(unittest.TestCase):
"transcript": "false", "exon": "false", "domain_2": "true", "function": "false", "function_details": "true"}
strains = {"mouse": ["S1", "S2", "S3", "S4", "S5"], "rat": []}
expected_results = ([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore',
- 'Domain 1', 'Domain 2', 'Details'],
- ['S1', 'S2', 'S3', 'S4', 'S5']], 5,
- ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles',
+ 'Domain 1', 'Domain 2', 'Details'],
+ ['S1', 'S2', 'S3', 'S4', 'S5']], 5,
+ ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles',
'conservation_score', 'domain_1', 'domain_2',
'function_details', 'S1', 'S2', 'S3', 'S4', 'S5'])
@@ -33,7 +33,7 @@ class TestSnpBrowser(unittest.TestCase):
variant_type="InDel", strains=strains, species="rat", empty_columns=[])
expected_results_with_indel = (
['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start',
- 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0,
+ 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0,
['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s',
'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'])
diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py
index 69977146..9d988aea 100644
--- a/wqflask/tests/unit/wqflask/test_server_side.py
+++ b/wqflask/tests/unit/wqflask/test_server_side.py
@@ -17,8 +17,8 @@ class TestServerSideTableTests(unittest.TestCase):
def test_get_page(self):
rows_count = 3
table_rows = [
- {'first': 'd', 'second': 4, 'third': 'zz'},
- {'first': 'b', 'second': 2, 'third': 'aa'},
+ {'first': 'd', 'second': 4, 'third': 'zz'},
+ {'first': 'b', 'second': 2, 'third': 'aa'},
{'first': 'c', 'second': 1, 'third': 'ss'},
]
headers = ['first', 'second', 'third']
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index d540c96e..816bc4df 100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -33,5 +33,3 @@ class Struct:
def __repr__(self):
return '{%s}' % str(', '.join('%s : %s' % (k, repr(v)) for
(k, v) in list(self.__dict__.items())))
-
-
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index 09100bd9..c0629b5d 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -98,4 +98,3 @@ class ConvertGenoFile:
print("WARNING:", genotype.upper())
this_marker.genotypes.append("NA")
self.markers.append(this_marker.__dict__)
-
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index 712517a3..a2bf3085 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -50,4 +50,4 @@ from wqflask import db_info
from wqflask import user_login
from wqflask import user_session
-import wqflask.views
+import wqflask.views
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index c22b44a9..e4a3fb77 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -140,5 +140,3 @@ def initialize_parameters(start_vars, dataset, this_trait):
mapping_params['perm_check'] = False
return mapping_params
-
-
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index e7dfa4e0..f7d52ca3 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -59,13 +59,13 @@ def get_species_info(species_name, file_format="json"):
WHERE (Name="{0}" OR FullName="{0}" OR SpeciesName="{0}");""".format(species_name))
the_species = results.fetchone()
- species_dict = {
+ species_dict = {
"Id": the_species[0],
"Name": the_species[1],
"FullName": the_species[2],
"TaxonomyId": the_species[3]
}
-
+
return flask.jsonify(species_dict)
@@ -639,7 +639,7 @@ def trait_sample_data(dataset_name, trait_name, file_format="json"):
return flask.jsonify(sample_list)
else:
- return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+ return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
@app.route("/api/v_{}/trait/<path:dataset_name>/<path:trait_name>".format(version))
@@ -685,7 +685,7 @@ def get_trait_info(dataset_name, trait_name, file_format="json"):
# ZS: Check if the user input the dataset_name as BXDPublish, etc (which is always going to be the group name + "Publish"
if "Publish" in dataset_name:
dataset_name = dataset_name.replace("Publish", "")
-
+
group_id = get_group_id(dataset_name)
pheno_query = """
SELECT
@@ -898,7 +898,7 @@ def get_dataset_trait_ids(dataset_name, start_vars):
data_type = "Publish"
dataset_name = dataset_name.replace("Publish", "")
dataset_id = get_group_id(dataset_name)
-
+
query = """
SELECT
PublishXRef.PhenotypeId, PublishXRef.Id, InbredSet.InbredSetCode
@@ -949,9 +949,9 @@ def get_samplelist(dataset_name):
WHERE StrainXRef.StrainId = Strain.Id AND
StrainXRef.InbredSetId = {}
""".format(group_id)
-
+
results = g.db.execute(query).fetchall()
-
+
samplelist = [result[0] for result in results]
return samplelist
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 1fcf15f0..9fd89524 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -239,4 +239,3 @@ def change_collection_name():
g.user_session.change_collection_name(collection_id, new_name)
return new_name
-
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index 0fabb833..d86c8e16 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -45,7 +45,7 @@ class ComparisonBarChart:
# ZS: Getting initial group name before verifying all traits are in the same group in the following loop
this_group = self.trait_list[0][1].group.name
for trait_db in self.trait_list:
-
+
if trait_db[1].group.name != this_group:
self.insufficient_shared_samples = True
break
@@ -53,7 +53,7 @@ class ComparisonBarChart:
this_group = trait_db[1].group.name
this_trait = trait_db[0]
self.traits.append(this_trait)
-
+
this_sample_data = this_trait.data
for sample in this_sample_data:
@@ -79,7 +79,7 @@ class ComparisonBarChart:
self.js_data = dict(traits=[trait.name for trait in self.traits],
samples=self.all_sample_list,
sample_data=self.sample_data,)
-
+
def get_trait_db_obs(self, trait_db_list):
self.trait_list = []
@@ -95,4 +95,3 @@ class ComparisonBarChart:
self.trait_list.append((trait_ob, dataset_ob))
#print("trait_list:", self.trait_list)
-
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index f9a0ea11..4f756f58 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -68,7 +68,7 @@ class CorrScatterPlot:
slope_string = '%.3E' % slope
else:
slope_string = '%.3f' % slope
-
+
x_buffer = (max(vals_1) - min(vals_1)) * 0.1
y_buffer = (max(vals_2) - min(vals_2)) * 0.1
@@ -82,7 +82,7 @@ class CorrScatterPlot:
ry = stats.rankdata(vals_2)
self.rdata = []
self.rdata.append(rx.tolist())
- self.rdata.append(ry.tolist())
+ self.rdata.append(ry.tolist())
srslope, srintercept, srr_value, srp_value, srstd_err = stats.linregress(
rx, ry)
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index e75c4a85..8ee24246 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -680,4 +680,3 @@ def get_header_fields(data_type, corr_method):
'Sample p(r)']
return header_fields
-
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index aefb4453..59469428 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -324,7 +324,7 @@ def sortEigenVectors(vector):
A.append(item[0])
B.append(item[1])
sum = reduce(lambda x, y: x + y, A, 0.0)
- A = [x * 100.0 / sum for x in A]
+ A = [x * 100.0 / sum for x in A]
return [A, B]
except:
return []
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 48a82435..f4eafbe7 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -66,7 +66,7 @@ class CTL:
def addNode(self, gt):
node_dict = {'data': {'id': str(gt.name) + ":" + str(gt.dataset.name),
- 'sid': str(gt.name),
+ 'sid': str(gt.name),
'dataset': str(gt.dataset.name),
'label': gt.name,
'symbol': gt.symbol,
@@ -238,4 +238,3 @@ class CTL:
self.render_image(self.results)
sys.stdout.flush()
return(dict(template_vars))
-
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index c7558ed8..8d28fef0 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -135,5 +135,3 @@ def process_query_results(results):
}
return info_ob
-
-
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index fc93248a..0a1a597d 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -20,7 +20,7 @@ class Docs:
self.title = self.entry.capitalize()
self.content = ""
else:
-
+
self.title = result[0]
self.content = result[1].decode("utf-8")
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 5bd54f9d..2c180d49 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -1,6 +1,6 @@
import csv
import xlsxwriter
-import io
+import io
import datetime
import itertools
@@ -20,7 +20,7 @@ def export_search_results_csv(targs):
table_data = json.loads(targs['export_data'])
table_rows = table_data['rows']
-
+
now = datetime.datetime.now()
time_str = now.strftime('%H:%M_%d%B%Y')
if 'file_name' in targs:
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index fd12562f..fcd943ba 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -48,7 +48,7 @@ class SendToWebGestalt:
id_type = "entrezgene"
- self.hidden_vars = {
+ self.hidden_vars = {
'gene_list': "\n".join(gene_id_list),
'id_type': "entrezgene",
'ref_set': "genome",
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index aa11caa8..02eb66e5 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -125,7 +125,7 @@ class Heatmap:
webqtlConfig.GENERATED_IMAGE_DIR,
output_filename)
- os.system(reaper_command)
+ os.system(reaper_command)
reaper_results = parse_reaper_output(output_filename)
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index cadff080..e624a146 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -10,7 +10,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd',
'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID',
'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd']
-
+
# List All Species in the Gene Table
speciesDict = {}
results = g.db.execute("""
@@ -21,7 +21,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
for item in results:
speciesDict[item[0]] = item[1]
-
+
# List current Species and other Species
speciesId = speciesDict[species]
otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())]
@@ -45,7 +45,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
newdict = {}
for j, item in enumerate(fetchFields):
newdict[item] = result[j]
- # count SNPs if possible
+ # count SNPs if possible
if diffCol and species == 'mouse':
newdict["snpCount"] = g.db.execute("""
SELECT count(*)
@@ -58,17 +58,17 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
(newdict["TxEnd"] - newdict["TxStart"]) / 1000.0
else:
newdict["snpDensity"] = newdict["snpCount"] = 0
-
+
try:
newdict['GeneLength'] = 1000.0 * (newdict['TxEnd'] - newdict['TxStart'])
except:
pass
-
+
# load gene from other Species by the same name
for item in otherSpecies:
othSpec, othSpecId = item
newdict2 = {}
-
+
resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (", ".join(fetchFields),
othSpecId,
newdict["GeneSymbol"])).fetchone()
@@ -76,8 +76,8 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
if resultsOther:
for j, item in enumerate(fetchFields):
newdict2[item] = resultsOther[j]
-
- # count SNPs if possible, could be a separate function
+
+ # count SNPs if possible, could be a separate function
if diffCol and othSpec == 'mouse':
newdict2["snpCount"] = g.db.execute("""
SELECT count(*)
@@ -91,17 +91,15 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
(newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0
else:
newdict2["snpDensity"] = newdict2["snpCount"] = 0
-
+
try:
newdict2['GeneLength'] = 1000.0 * \
(newdict2['TxEnd'] - newdict2['TxStart'])
except:
pass
-
+
newdict['%sGene' % othSpec] = newdict2
-
+
GeneList.append(newdict)
return GeneList
-
-
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index f932498f..c51b7a9a 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -34,7 +34,7 @@ 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_" +
+ bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_" +
''.join(random.choice(string.ascii_uppercase + string.digits)
for _ in range(6))
)
@@ -44,8 +44,8 @@ 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 +
+ 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))
@@ -56,7 +56,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
if manhattan_plot != True:
opt_list.append("--interval 1")
- reaper_command = (REAPER_COMMAND +
+ reaper_command = (REAPER_COMMAND +
' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'),
genofile_name,
@@ -81,7 +81,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
suggestive = permu_vals[int(num_perm * 0.37 - 1)]
significant = permu_vals[int(num_perm * 0.95 - 1)]
- return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals,
+ return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals,
[output_filename, permu_filename, bootstrap_filename])
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 741d6c23..b3c9fddf 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -300,7 +300,7 @@ def add_categorical_covar(cross, covar_as_string, i):
ro.r('the_cross$pheno <- cbind(pheno, ' + \
col_name + ' = newcovar[,' + str(x) + '])')
col_names.append(col_name)
- #logger.info("loop" + str(x) + "done");
+ #logger.info("loop" + str(x) + "done");
logger.info("returning from add_categorical_covar")
return ro.r["the_cross"], col_names
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 36d4cd61..61f3b202 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -142,5 +142,5 @@ def get_group_names(group_masks):
group_name = get_group_info(group_id)['name']
this_mask['name'] = group_name
group_masks_with_names[group_id] = this_mask
-
+
return group_masks_with_names
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 273a97a4..0d2fb2f8 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -343,4 +343,3 @@ def get_aliases(symbol_list, species):
search_terms.append(the_search_term)
return search_terms
-
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
index 8b3a4faa..8ca3a9eb 100644
--- a/wqflask/wqflask/server_side.py
+++ b/wqflask/wqflask/server_side.py
@@ -30,7 +30,7 @@ class ServerSideTable:
self.rows_count = rows_count
self.table_rows = table_rows
self.header_data_names = header_data_names
-
+
self.sort_rows()
self.paginate_rows()
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index e98cfb71..5b7a663c 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -494,10 +494,10 @@ class SnpBrowser:
function_details = function_details + ", Coding Region Unknown"
self.empty_columns['function_details'] = "true"
-
+
#[snp_href, chr, mb_formatted, alleles, snp_source_cell, conservation_score, gene_name_cell, transcript_href, exon, domain_1, domain_2, function, function_details]
- base_color_dict = {"A": "#C33232", "C": "#1569C7", "T": "#CFCF32", "G": "#32C332",
+ base_color_dict = {"A": "#C33232", "C": "#1569C7", "T": "#CFCF32", "G": "#32C332",
"t": "#FF6", "c": "#5CB3FF", "a": "#F66", "g": "#CF9", ":": "#FFFFFF", "-": "#FFFFFF", "?": "#FFFFFF"}
the_bases = []
@@ -735,7 +735,7 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None):
if empty_columns['function_details'] == "false":
empty_field_count += 1
header_fields[0].remove('Details')
-
+
for col in empty_columns.keys():
if empty_columns[col] == "false":
header_data_names.remove(col)
@@ -952,4 +952,3 @@ def check_if_in_gene(species_id, chr, mb):
return [result[0], result[1]]
else:
return ""
-
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 708d43d2..bfaed9c2 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -45,10 +45,10 @@ def encode_password(pass_gen_fields, unencrypted_password):
salt = pass_gen_fields['salt']
else:
salt = bytes(pass_gen_fields['salt'], "utf-8")
- encrypted_password = pbkdf2.pbkdf2_hex(str(unencrypted_password),
+ encrypted_password = pbkdf2.pbkdf2_hex(str(unencrypted_password),
salt,
- pass_gen_fields['iterations'],
- pass_gen_fields['keylength'],
+ pass_gen_fields['iterations'],
+ pass_gen_fields['keylength'],
pass_gen_fields['hashfunc'])
pass_gen_fields.pop("unencrypted_password", None)
@@ -111,7 +111,7 @@ def get_signed_session_id(user):
key = UserSession.user_cookie_name + ":" + session_id
Redis.hmset(key, session)
Redis.expire(key, THREE_DAYS)
-
+
return session_id_signed
@@ -207,7 +207,7 @@ def login():
UserSession.user_cookie_name, session_id_signed, max_age=None)
else:
flash("Something went unexpectedly wrong.", "alert-danger")
- response = make_response(redirect(url_for('index_page')))
+ response = make_response(redirect(url_for('index_page')))
return response
else:
user_details = get_user_by_unique_column(
@@ -276,13 +276,13 @@ 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") if github_user["name"] else "None",
+ "user_id": str(uuid.uuid4()),
+ "name": github_user["name"].encode("utf-8") if github_user["name"] else "None",
"github_id": github_user["id"],
- "user_url": github_user["html_url"].encode("utf-8"),
- "login_type": "github",
- "organization": "",
- "active": 1,
+ "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"])
@@ -308,8 +308,8 @@ def orcid_oauth2():
url = "/n/login"
if code:
data = {
- "client_id": ORCID_CLIENT_ID,
- "client_secret": ORCID_CLIENT_SECRET,
+ "client_id": ORCID_CLIENT_ID,
+ "client_secret": ORCID_CLIENT_SECRET,
"grant_type": "authorization_code",
"redirect_uri": GN2_BRANCH_URL + "n/login/orcid_oauth2",
"code": code
@@ -321,13 +321,13 @@ def orcid_oauth2():
user_details = get_user_by_unique_column("orcid", result_dict["orcid"])
if user_details == None:
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,
+ "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
}
save_user(user_details, user_details["user_id"])
@@ -374,7 +374,7 @@ def send_forgot_password_email(verification_email):
key_prefix = "forgot_password_code"
subject = "GeneNetwork password reset"
fromaddr = "no-reply@genenetwork.org"
-
+
verification_code = str(uuid.uuid4())
key = key_prefix + ":" + verification_code
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 6ccb2e80..963288b3 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -318,5 +318,3 @@ class UserSession:
# And more importantly delete the redis record
Redis.delete(self.redis_key)
self.logged_in = False
-
-