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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 4fd3462fc8
commit 6cedc3c14d
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 #%% command line args
arg_parser = argparse.ArgumentParser() arg_parser = argparse.ArgumentParser()
arg_parser.add_argument('-d', '--drug', help='drug name', default = None) 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() args = arg_parser.parse_args()
#======================================================================= #=======================================================================
#%% variable assignment: input and output paths & filenames #%% variable assignment: input and output paths & filenames
@ -82,7 +84,7 @@ gene = 'pncA'
gene_match = gene + '_p.' gene_match = gene + '_p.'
print('mut pattern for gene', gene, ':', gene_match) 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) print('nsSNP for gene', gene, ':', nssnp_match)
wt_regex = gene_match.lower()+'(\w{3})' wt_regex = gene_match.lower()+'(\w{3})'

6
scripts/dssp_df.py
View file

@ -52,7 +52,7 @@ drug = args.drug
gene = args.gene gene = args.gene
gene_match = gene + '_p.' gene_match = gene + '_p.'
data_dir = args.datadir datadir = args.datadir
indir = args.input_dir indir = args.input_dir
outdir = args.output_dir outdir = args.output_dir
@ -63,9 +63,7 @@ DEBUG = args.debug
#============= #=============
# directories # directories
#============= #=============
if data_dir: if not datadir:
datadir = data_dir
else:
datadir = homedir + '/' + 'git/Data' datadir = homedir + '/' + 'git/Data'
if not indir: if not indir:

6
scripts/kd_df.py
View file

@ -60,7 +60,7 @@ drug = args.drug
gene = args.gene gene = args.gene
gene_match = gene + '_p.' gene_match = gene + '_p.'
data_dir = args.datadir datadir = args.datadir
indir = args.input_dir indir = args.input_dir
outdir = args.output_dir outdir = args.output_dir
@ -72,9 +72,7 @@ DEBUG = args.debug
#============ #============
# directories # directories
#============ #============
if data_dir: if not datadir:
datadir = data_dir
else:
datadir = homedir + '/' + 'git/Data' datadir = homedir + '/' + 'git/Data'
if not indir: if not indir:

7
scripts/rd_df.py
View file

@ -51,7 +51,7 @@ drug = args.drug
gene = args.gene gene = args.gene
gene_match = gene + '_p.' gene_match = gene + '_p.'
data_dir = args.datadir datadir = args.datadir
indir = args.input_dir indir = args.input_dir
outdir = args.output_dir outdir = args.output_dir
@ -62,9 +62,7 @@ DEBUG = args.debug
#============ #============
# directories # directories
#============ #============
if data_dir: if not datadir:
datadir = data_dir
else:
datadir = homedir + '/' + 'git/Data' datadir = homedir + '/' + 'git/Data'
if not indir: if not indir:
@ -79,7 +77,6 @@ if not outdir:
if rd_filename: if rd_filename:
in_filename_rd = rd_filename in_filename_rd = rd_filename
else: else:
#in_filename_rd = '3pl1_rd.tsv'
in_filename_rd = gene.lower() + '_rd.tsv' in_filename_rd = gene.lower() + '_rd.tsv'
infile_rd = outdir + '/' + in_filename_rd infile_rd = outdir + '/' + in_filename_rd