From c80faef0bf3310b663d93ce68c141cfcb11bb637 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Fri, 10 Jul 2020 12:37:41 +0100
Subject: [PATCH] refactoring or_kin script minor changes only

---
 scripts/data_extraction.py | 6 ++++--
 scripts/dssp_df.py         | 6 ++----
 scripts/kd_df.py           | 6 ++----
 scripts/rd_df.py           | 7 ++-----
 4 files changed, 10 insertions(+), 15 deletions(-)

diff --git a/scripts/data_extraction.py b/scripts/data_extraction.py
index e9500e3..a682fbc 100755
--- a/scripts/data_extraction.py
+++ b/scripts/data_extraction.py
@@ -69,7 +69,9 @@ from tidy_split import tidy_split
 #%% command line args
 arg_parser = argparse.ArgumentParser()
 arg_parser.add_argument('-d', '--drug', help='drug name', default = None)
-arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = None) # case sensitive
+arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = None)
+
+
 args = arg_parser.parse_args()
 #=======================================================================
 #%% variable assignment: input and output paths & filenames
@@ -82,7 +84,7 @@ gene = 'pncA'
 gene_match = gene + '_p.'
 print('mut pattern for gene', gene, ':',  gene_match)
 
-nssnp_match = gene_match+'[A-Z]{3}[0-9]+[A-Z]{3}'
+nssnp_match = gene_match +'[A-Z]{3}[0-9]+[A-Z]{3}'
 print('nsSNP for gene', gene, ':',  nssnp_match)
 
 wt_regex = gene_match.lower()+'(\w{3})'
diff --git a/scripts/dssp_df.py b/scripts/dssp_df.py
index 3d5dfcd..966acaf 100755
--- a/scripts/dssp_df.py
+++ b/scripts/dssp_df.py
@@ -52,7 +52,7 @@ drug         = args.drug
 gene         = args.gene
 gene_match   = gene + '_p.'
 
-data_dir     = args.datadir
+datadir     = args.datadir
 indir        = args.input_dir
 outdir       = args.output_dir
 
@@ -63,9 +63,7 @@ DEBUG        = args.debug
 #=============
 # directories
 #=============
-if data_dir:
-    datadir = data_dir
-else:
+if not datadir:
     datadir = homedir + '/' + 'git/Data'
 
 if not indir:
diff --git a/scripts/kd_df.py b/scripts/kd_df.py
index e36d660..53b1264 100755
--- a/scripts/kd_df.py
+++ b/scripts/kd_df.py
@@ -60,7 +60,7 @@ drug = args.drug
 gene = args.gene
 gene_match = gene + '_p.'
 
-data_dir     = args.datadir
+datadir     = args.datadir
 indir        = args.input_dir
 outdir       = args.output_dir
 
@@ -72,9 +72,7 @@ DEBUG        = args.debug
 #============
 # directories
 #============
-if data_dir:
-    datadir = data_dir
-else:
+if not datadir:
     datadir = homedir + '/' + 'git/Data'
 
 if not indir:
diff --git a/scripts/rd_df.py b/scripts/rd_df.py
index 81863b5..8794792 100755
--- a/scripts/rd_df.py
+++ b/scripts/rd_df.py
@@ -51,7 +51,7 @@ drug = args.drug
 gene = args.gene
 gene_match = gene + '_p.'
 
-data_dir     = args.datadir
+datadir     = args.datadir
 indir        = args.input_dir
 outdir       = args.output_dir
 
@@ -62,9 +62,7 @@ DEBUG        = args.debug
 #============
 # directories
 #============
-if data_dir:
-    datadir = data_dir
-else:
+if not datadir:
     datadir = homedir + '/' + 'git/Data'
 
 if not indir:
@@ -79,7 +77,6 @@ if not outdir:
 if rd_filename:
     in_filename_rd = rd_filename
 else:
-    #in_filename_rd = '3pl1_rd.tsv'
     in_filename_rd = gene.lower() + '_rd.tsv'
  
 infile_rd = outdir + '/' + in_filename_rd