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inlcuded the revised master file for 35k isolates

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Tanushree Tunstall 2020-06-16 11:39:11 +01:00
parent e2f319ba42
commit e21635fe02
2 changed files with 8 additions and 8 deletions
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13
scripts/data_extraction.py
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@ -47,15 +47,13 @@ from reference_dict import my_aa_dict # CHECK DIR STRUC THERE!
#======================================================================= #=======================================================================
#%% command line args #%% command line args
arg_parser = argparse.ArgumentParser() arg_parser = argparse.ArgumentParser()
#arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide') arg_parser.add_argument('-d', '--drug', help='drug name', default = None)
#arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = None) # 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
args = arg_parser.parse_args() args = arg_parser.parse_args()
#======================================================================= #=======================================================================
#%% variable assignment: input and output paths & filenames #%% variable assignment: input and output paths & filenames
#drug = #drug = 'pyrazinamide'
#gene = ' #gene = 'pncA'
drug = args.drug drug = args.drug
gene = args.gene gene = args.gene
@ -82,7 +80,8 @@ datadir = homedir + '/' + 'git/Data'
#======= #=======
# input # 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 infile = datadir + '/' + in_filename
print('Input file: ', infile print('Input file: ', infile
, '\n============================================================') , '\n============================================================')

3
scripts/pipeline.ini
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@ -1,6 +1,7 @@
[extractor] [extractor]
data_dir = /home/tanu/git/Data 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: # Relative Paths. Per-drug paths will be created like:
# #