autopep8: Fix E501

5 files changed, 31 insertions, 15 deletions

diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index 5b2369c9..a1712500 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -83,7 +83,8 @@ class ConvertGenoFile:
                 genotypes = row_items[2:]
             for item_count, genotype in enumerate(genotypes):
                 if genotype.upper().strip() in self.configurations:
-                    this_marker.genotypes.append(self.configurations[genotype.upper().strip()])
+                    this_marker.genotypes.append(
+                        self.configurations[genotype.upper().strip()])
                 else:
                     this_marker.genotypes.append("NA")
 
@@ -106,9 +107,11 @@ class ConvertGenoFile:
         with open(self.output_files[2], "w") as snp_fh:
             for marker in self.markers:
                 if self.mb_exists:
-                    snp_fh.write(marker['name'] + ", " + str(int(float(marker['Mb']) * 1000000)) + ", " + marker['chr'] + "\n")
+                    snp_fh.write(
+                        marker['name'] + ", " + str(int(float(marker['Mb']) * 1000000)) + ", " + marker['chr'] + "\n")
                 else:
-                    snp_fh.write(marker['name'] + ", " + str(int(float(marker['cM']) * 1000000)) + ", " + marker['chr'] + "\n")
+                    snp_fh.write(
+                        marker['name'] + ", " + str(int(float(marker['cM']) * 1000000)) + ", " + marker['chr'] + "\n")
 
     def get_sample_list(self, row_contents):
         self.sample_list = []
@@ -160,10 +163,14 @@ class ConvertGenoFile:
             group_name = ".".join(input_file.split('.')[:-1])
             if group_name == "HSNIH-Palmer":
                 continue
-            geno_output_file = os.path.join(new_directory, group_name + "_geno.txt")
-            pheno_output_file = os.path.join(new_directory, group_name + "_pheno.txt")
-            snp_output_file = os.path.join(new_directory, group_name + "_snps.txt")
-            output_files = [geno_output_file, pheno_output_file, snp_output_file]
+            geno_output_file = os.path.join(
+                new_directory, group_name + "_geno.txt")
+            pheno_output_file = os.path.join(
+                new_directory, group_name + "_pheno.txt")
+            snp_output_file = os.path.join(
+                new_directory, group_name + "_snps.txt")
+            output_files = [geno_output_file,
+                pheno_output_file, snp_output_file]
             print("%s -> %s" % (
                 os.path.join(old_directory, input_file), geno_output_file))
             convertob = ConvertGenoFile(input_file, output_files)
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 583a06e1..484336a6 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -120,14 +120,16 @@ def get_types(groups):
                 else:
                     if not phenotypes_exist(group_name) and not genotypes_exist(group_name):
                         types[species].pop(group_name, None)
-                        groups[species] = tuple(group for group in groups[species] if group[0] != group_name)
+                        groups[species] = tuple(
+                            group for group in groups[species] if group[0] != group_name)
             else:  # ZS: This whole else statement might be unnecessary, need to check
                 types_list = build_types(species, group_name)
                 if len(types_list) > 0:
                     types[species][group_name] = types_list
                 else:
                     types[species].pop(group_name, None)
-                    groups[species] = tuple(group for group in groups[species] if group[0] != group_name)
+                    groups[species] = tuple(
+                        group for group in groups[species] if group[0] != group_name)
     return types
 
 
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index 7cc60c9e..bed634fa 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -21,7 +21,9 @@ class GenerateKinshipMatrices:
         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 + " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name
+        gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + \
+            " -p " + self.pheno_file + \
+                " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name
         print("command:", gemma_command)
         os.system(gemma_command)
 
@@ -34,9 +36,12 @@ class GenerateKinshipMatrices:
             group_name = ".".join(input_file.split('.')[:-1])
             if group_name == "HSNIH-Palmer":
                 continue
-            geno_input_file = os.path.join(bimbam_dir, group_name + "_geno.txt")
-            pheno_input_file = os.path.join(bimbam_dir, group_name + "_pheno.txt")
-            convertob = GenerateKinshipMatrices(group_name, geno_input_file, pheno_input_file)
+            geno_input_file = os.path.join(
+                bimbam_dir, group_name + "_geno.txt")
+            pheno_input_file = os.path.join(
+                bimbam_dir, group_name + "_pheno.txt")
+            convertob = GenerateKinshipMatrices(
+                group_name, geno_input_file, pheno_input_file)
             try:
                 convertob.generate_kinship()
             except EmptyConfigurations as why:
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index ad3f2b72..7bdf2b53 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -100,7 +100,8 @@ class ConvertGenoFile:
                 genotypes = row_items[2:]
             for item_count, genotype in enumerate(genotypes):
                 if genotype.upper() in self.configurations:
-                    this_marker.genotypes.append(self.configurations[genotype.upper()])
+                    this_marker.genotypes.append(
+                        self.configurations[genotype.upper()])
                 else:
                     this_marker.genotypes.append("NA")
                 
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 1896bc52..ac7689f5 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -34,7 +34,8 @@ def create_dataframe(input_file):
     with open(input_file) as f:
         ncols = len(f.readline().split("\t"))
 
-    input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols)))
+    input_array = np.loadtxt(open(
+        input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols)))
     return pd.DataFrame(input_array)
 
 # This function taken from https://github.com/ShawnLYU/Quantile_Normalize