From 96da4d8ed50c0f1d2d1dcce1ef5d2eeca5d7d63f Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Tue, 16 Jun 2020 11:39:11 +0100
Subject: [PATCH] inlcuded the revised master file for 35k isolates

---
 scripts/data_extraction.py | 13 ++++++-------
 scripts/pipeline.ini       |  3 ++-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/scripts/data_extraction.py b/scripts/data_extraction.py
index 5c6f4c6..e734e55 100755
--- a/scripts/data_extraction.py
+++ b/scripts/data_extraction.py
@@ -47,15 +47,13 @@ from reference_dict import my_aa_dict # CHECK DIR STRUC THERE!
 #=======================================================================
 #%% command line args
 arg_parser = argparse.ArgumentParser()
-#arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
-#arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
-arg_parser.add_argument('-d', '--drug', help='drug name', default = 'TESTDRUG')
-arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = 'testGene') # case sensitive
+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
 args = arg_parser.parse_args()
 #=======================================================================
 #%% variable assignment: input and output paths & filenames
-#drug = 
-#gene = '
+#drug = 'pyrazinamide'
+#gene = 'pncA'
 
 drug = args.drug
 gene = args.gene
@@ -82,7 +80,8 @@ datadir = homedir + '/' + 'git/Data'
 #=======
 # input
 #=======
-in_filename  = 'original_tanushree_data_v2.csv'
+#in_filename  = 'original_tanushree_data_v2.csv'
+in_filename  = 'mtb_gwas_v3.csv'
 infile = datadir + '/' + in_filename
 print('Input file: ', infile
       , '\n============================================================')
diff --git a/scripts/pipeline.ini b/scripts/pipeline.ini
index e097788..523d6f3 100644
--- a/scripts/pipeline.ini
+++ b/scripts/pipeline.ini
@@ -1,6 +1,7 @@
 [extractor]
 data_dir = /home/tanu/git/Data
-master_file = original_tanushree_data_v2.csv
+#master_file = original_tanushree_data_v2.csv
+master_file = mtb_gwas_v3.csv
 
 # Relative Paths. Per-drug paths will be created like:
 #