From 8ef936889bdf722662a427a7169e1fa5c8c0062e Mon Sep 17 00:00:00 2001
From: yashjanidev <99663141+yashjanidev@users.noreply.github.com>
Date: Sat, 4 Nov 2023 21:11:08 +0530
Subject: [PATCH 1/2] Update vcfPrepper.py

Changed variable fileFolderPath > vcfFileFolderPath.

because vcfFileFolderPath is better name convention.

and Added some comments so new user can relate with import files
---
 utilities/vcfPrepper.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/utilities/vcfPrepper.py b/utilities/vcfPrepper.py
index 82e75a8f2..37f9c9f73 100644
--- a/utilities/vcfPrepper.py
+++ b/utilities/vcfPrepper.py
@@ -2,9 +2,9 @@
 import subprocess
 import sys
 
-fileFolderPath = "C:\\snpEff\\simple\\38"
-outputFolderPath = "C:\\snpEff\\output"
-snpEffPath = "C:\\snpEff"
+vcfFileFolderPath = "C:\\snpEff\\simple\\38" # Path where VCF file is present
+outputFolderPath = "C:\\snpEff\\output"      # Here, output will generate
+snpEffPath = "C:\\snpEff"                    # Path of snpEff folder
 databasePath = "C:\\snpEff\\gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz"
 
 genome = 'GRCh38.p13'
@@ -22,9 +22,9 @@
 
 os.chdir(snpEffPath)
 
-for vcfFile in os.listdir(fileFolderPath):
+for vcfFile in os.listdir(vcfFileFolderPath):
     print('in file: ' + vcfFile)
-    filePath = fileFolderPath + '\\' + vcfFile
+    filePath = vcfFileFolderPath + '\\' + vcfFile
     outputPath = outputFolderPath + '\\' + vcfFile
     snpEffCmd = ['java', '-jar', snpEffJarPath] + ['-o', 'vcf'] + [genome, filePath]
 

From fe92e1d3f42e8a03a15732e47fa5cff333bd87fd Mon Sep 17 00:00:00 2001
From: yashjanidev <99663141+yashjanidev@users.noreply.github.com>
Date: Sun, 5 Nov 2023 07:47:14 +0530
Subject: [PATCH 2/2] Update vcfPrepper.py

Followed Flake8 Rules for comments.
---
 utilities/vcfPrepper.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/utilities/vcfPrepper.py b/utilities/vcfPrepper.py
index 37f9c9f73..3f11d9be4 100644
--- a/utilities/vcfPrepper.py
+++ b/utilities/vcfPrepper.py
@@ -2,9 +2,9 @@
 import subprocess
 import sys
 
-vcfFileFolderPath = "C:\\snpEff\\simple\\38" # Path where VCF file is present
-outputFolderPath = "C:\\snpEff\\output"      # Here, output will generate
-snpEffPath = "C:\\snpEff"                    # Path of snpEff folder
+vcfFileFolderPath = "C:\\snpEff\\simple\\38"  # Path where VCF file is present
+outputFolderPath = "C:\\snpEff\\output"  # Here, output will generate
+snpEffPath = "C:\\snpEff"  # Path of snpEff folder
 databasePath = "C:\\snpEff\\gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz"
 
 genome = 'GRCh38.p13'