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refactoring or_kin script minor changes only

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This commit is contained in:
Tanushree Tunstall 2020-07-10 12:37:41 +01:00
parent aaf3f5e084
commit c80faef0bf
4 changed files with 10 additions and 15 deletions
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6
scripts/data_extraction.py
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@ -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})'