autopep8: Fix W291, W292, W293, W391

4 files changed, 24 insertions, 24 deletions

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)