about summary refs log tree commit diff
path: root/wqflask/maintenance
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask/maintenance')
-rw-r--r--wqflask/maintenance/convert_dryad_to_bimbam.py3
-rw-r--r--wqflask/maintenance/convert_geno_to_bimbam.py4
-rw-r--r--wqflask/maintenance/gen_select_dataset.py5
-rw-r--r--wqflask/maintenance/generate_kinship_from_bimbam.py1
-rw-r--r--wqflask/maintenance/generate_probesetfreeze_file.py7
-rw-r--r--wqflask/maintenance/geno_to_json.py6
-rw-r--r--wqflask/maintenance/get_group_samplelists.py3
-rw-r--r--wqflask/maintenance/print_benchmark.py4
-rw-r--r--wqflask/maintenance/quantile_normalize.py6
-rw-r--r--wqflask/maintenance/set_resource_defaults.py7
10 files changed, 42 insertions, 4 deletions
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
index 8eab66e8..e417c280 100644
--- a/wqflask/maintenance/convert_dryad_to_bimbam.py
+++ b/wqflask/maintenance/convert_dryad_to_bimbam.py
@@ -55,15 +55,18 @@ def read_dryad_file(filename):
     #            
     # return geno_rows
 
+
 def write_bimbam_files(geno_rows):
     with open('/home/zas1024/cfw_data/CFW_geno.txt', 'w') as geno_fh:
         for row in geno_rows:
             geno_fh.write(", ".join(row) + "\n")
 
+
 def convert_dryad_to_bimbam(filename):
     geno_file_rows = read_dryad_file(filename)
     write_bimbam_files(geno_file_rows)
 
+
 if __name__ == "__main__":
     input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
     convert_dryad_to_bimbam(input_filename)
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index dc01cbb3..5b2369c9 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -20,8 +20,10 @@ import simplejson as json
 
 from pprint import pformat as pf
 
+
 class EmptyConfigurations(Exception): pass
 
+
 class Marker:
     def __init__(self):
         self.name = None
@@ -30,6 +32,7 @@ class Marker:
         self.Mb = None
         self.genotypes = []
 
+
 class ConvertGenoFile:
 
     def __init__(self, input_file, output_files):
@@ -178,6 +181,7 @@ class ConvertGenoFile:
                 print("    Row is:", convertob.latest_row_value)
                 break
 
+
 if __name__ == "__main__":
     Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
     New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/bimbam"""
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index f480d63f..583a06e1 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -55,6 +55,7 @@ from pprint import pformat as pf
 
 #conn = Engine.connect()
 
+
 def parse_db_uri():
     """Converts a database URI to the db name, host name, user name, and password"""
 
@@ -143,6 +144,7 @@ def phenotypes_exist(group_name):
     else:
         return False
 
+
 def genotypes_exist(group_name):
     #print("group_name:", group_name)
     Cursor.execute("""select Name from GenoFreeze
@@ -156,6 +158,7 @@ def genotypes_exist(group_name):
     else:
         return False
 
+
 def build_types(species, group):
     """Fetches tissues
 
@@ -184,6 +187,7 @@ def build_types(species, group):
 
     return results
 
+
 def get_datasets(types):
     """Build datasets list"""
     datasets = {}
@@ -308,6 +312,7 @@ def _test_it():
     datasets = build_datasets("Mouse", "BXD", "Hippocampus")
     #print("build_datasets:", pf(datasets))
 
+
 if __name__ == '__main__':
     Conn = MySQLdb.Connect(**parse_db_uri())
     Cursor = Conn.cursor()
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index 664e9e48..7cc60c9e 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -13,6 +13,7 @@ sys.path.append("..")
 import os
 import glob
 
+
 class GenerateKinshipMatrices:
     def __init__(self, group_name, geno_file, pheno_file):
         self.group_name = group_name
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
index b1e41e9a..bd9c2ab4 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -23,10 +23,12 @@ def get_cursor():
     cursor = con.cursor()
     return cursor
 
+
 def show_progress(process, counter):
     if counter % 1000 == 0:
         print("{}: {}".format(process, counter))
 
+
 def get_strains(cursor):
     cursor.execute("""select Strain.Name
                       from Strain, StrainXRef, InbredSet
@@ -42,6 +44,7 @@ def get_strains(cursor):
 
     return strains
 
+
 def get_probeset_vals(cursor, dataset_name):
     cursor.execute(""" select ProbeSet.Id, ProbeSet.Name
                 from ProbeSetXRef,
@@ -77,6 +80,7 @@ def get_probeset_vals(cursor, dataset_name):
 
     return probeset_vals
 
+
 def trim_strains(strains, probeset_vals):
     trimmed_strains = []
     #print("probeset_vals is:", pf(probeset_vals))
@@ -89,6 +93,7 @@ def trim_strains(strains, probeset_vals):
     print("trimmed_strains:", pf(trimmed_strains))
     return trimmed_strains
 
+
 def write_data_matrix_file(strains, probeset_vals, filename):
     with open(filename, "wb") as fh:
         csv_writer = csv.writer(fh, delimiter=",", quoting=csv.QUOTE_ALL)
@@ -103,6 +108,7 @@ def write_data_matrix_file(strains, probeset_vals, filename):
             csv_writer.writerow(row_data)
             show_progress("Writing", counter)
 
+
 def main():
     filename = os.path.expanduser("~/gene/wqflask/maintenance/" +
                 "ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2" +
@@ -117,5 +123,6 @@ def main():
     trimmed_strains = trim_strains(strains, probeset_vals)
     write_data_matrix_file(trimmed_strains, probeset_vals, filename)
 
+
 if __name__ == '__main__':
     main()
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index fa0dcebd..ad3f2b72 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -25,10 +25,10 @@ from pprint import pformat as pf
 
 #from utility.tools import flat_files
 
+
 class EmptyConfigurations(Exception): pass
 
         
-
 class Marker:
     def __init__(self):
         self.name = None
@@ -37,6 +37,7 @@ class Marker:
         self.Mb = None
         self.genotypes = []
 
+
 class ConvertGenoFile:
 
     def __init__(self, input_file, output_file):
@@ -78,7 +79,6 @@ class ConvertGenoFile:
             # elif self.file_type == "snps":
             #    self.process_snps_file()
 
-
     def process_csv(self):
         for row_count, row in enumerate(self.process_rows()):
             row_items = row.split("\t")
@@ -121,7 +121,6 @@ class ConvertGenoFile:
                     
             # self.output_fh.write("\n")
 
-
     def process_rows(self):
         for self.latest_row_pos, row in enumerate(self.input_fh):
             # if self.input_file.endswith(".geno.gz"):
@@ -182,7 +181,6 @@ class ConvertGenoFile:
     #    convertob = ConvertGenoFile(input_file, output_file)
         
 
-
 if __name__ == "__main__":
     Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
     New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/json"""
diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
index 3f9d0278..0a450d3f 100644
--- a/wqflask/maintenance/get_group_samplelists.py
+++ b/wqflask/maintenance/get_group_samplelists.py
@@ -4,12 +4,14 @@ import gzip
 
 from base import webqtlConfig
 
+
 def get_samplelist(file_type, geno_file):
     if file_type == "geno":
         return get_samplelist_from_geno(geno_file)
     elif file_type == "plink":
         return get_samplelist_from_plink(geno_file)
 
+
 def get_samplelist_from_geno(genofilename):
     if os.path.isfile(genofilename + '.gz'):
         genofilename += '.gz'
@@ -33,6 +35,7 @@ def get_samplelist_from_geno(genofilename):
         samplelist = headers[3:]
     return samplelist
 
+
 def get_samplelist_from_plink(genofilename):
     genofile = open(genofilename)
 
diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py
index a1046c86..9d12da8a 100644
--- a/wqflask/maintenance/print_benchmark.py
+++ b/wqflask/maintenance/print_benchmark.py
@@ -15,15 +15,18 @@ class TheCounter:
         self.time_took = time.time() - start_time
         TheCounter.Counters[self.__class__.__name__] = self.time_took
 
+
 class PrintAll(TheCounter):
     def print_it(self, counter):
         print(counter)
 
+
 class PrintSome(TheCounter):
     def print_it(self, counter):
         if counter % 1000 == 0:
             print(counter)
 
+
 class PrintNone(TheCounter):
     def print_it(self, counter):
         pass
@@ -37,5 +40,6 @@ def new_main():
 
     print(pf(TheCounter.Counters))
 
+
 if __name__ == '__main__':
     new_main()
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 6751a8e5..1896bc52 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -14,6 +14,7 @@ from wqflask import app
 from utility.elasticsearch_tools import get_elasticsearch_connection
 from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT, SQL_URI
 
+
 def parse_db_uri():
     """Converts a database URI to the db name, host name, user name, and password"""
 
@@ -28,6 +29,7 @@ def parse_db_uri():
     print(db_conn_info)
     return db_conn_info
 
+
 def create_dataframe(input_file):
     with open(input_file) as f:
         ncols = len(f.readline().split("\t"))
@@ -36,6 +38,8 @@ def create_dataframe(input_file):
     return pd.DataFrame(input_array)
 
 # This function taken from https://github.com/ShawnLYU/Quantile_Normalize
+
+
 def quantileNormalize(df_input):
     df = df_input.copy()
     # compute rank
@@ -50,6 +54,7 @@ def quantileNormalize(df_input):
         df[col] = [rank[i] for i in t]
     return df
 
+
 def set_data(dataset_name):
     orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt"
 
@@ -95,6 +100,7 @@ def set_data(dataset_name):
                     }
                 }
 
+
 if __name__ == '__main__':
     Conn = MySQLdb.Connect(**parse_db_uri())
     Cursor = Conn.cursor()
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 286094dd..c6c4f44c 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -37,6 +37,7 @@ import urllib.parse
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 def parse_db_uri():
     """Converts a database URI to the db name, host name, user name, and password"""
 
@@ -51,6 +52,7 @@ def parse_db_uri():
     print(db_conn_info)
     return db_conn_info
 
+
 def insert_probeset_resources(default_owner_id):
     current_resources = Redis.hgetall("resources")
     Cursor.execute("""  SELECT
@@ -77,6 +79,7 @@ def insert_probeset_resources(default_owner_id):
 
         add_resource(resource_ob, update=False)
 
+
 def insert_publish_resources(default_owner_id):
     current_resources = Redis.hgetall("resources")
     Cursor.execute("""  SELECT 
@@ -110,6 +113,7 @@ def insert_publish_resources(default_owner_id):
         else:
             continue
 
+
 def insert_geno_resources(default_owner_id):
     current_resources = Redis.hgetall("resources")
     Cursor.execute("""  SELECT
@@ -139,6 +143,7 @@ def insert_geno_resources(default_owner_id):
 
         add_resource(resource_ob, update=False)
 
+
 def insert_resources(default_owner_id):
     current_resources = get_resources()
     print("START")
@@ -149,6 +154,7 @@ def insert_resources(default_owner_id):
     insert_probeset_resources(default_owner_id)
     print("AFTER PROBESET")
 
+
 def main():
     """Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
 
@@ -158,6 +164,7 @@ def main():
 
     insert_resources(owner_id)
 
+
 if __name__ == '__main__':
     Conn = MySQLdb.Connect(**parse_db_uri())
     Cursor = Conn.cursor()
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-10-06 21:13:07 +0000