script to combine all ors

scripts/af_or_calcs.R

@@ -59,7 +59,7 @@ cat(paste0('Reading infile2: gene associated metadata:', infile_metadata))
 # outdir = 'git/Data/pyrazinamide/output'
 outdir = paste0('~/git/Data', '/', drug, '/', 'output')
 #out_filename = paste0(tolower(gene), '_meta_data_with_AF_OR.csv')
-out_filename = paste0(tolower(gene), '_AF_OR.csv')
+out_filename = paste0(tolower(gene), '_af_or.csv')
 outfile = paste0(outdir, '/', out_filename)
 cat(paste0('Output file with full path:', outfile))
 #%% end of variable assignment for input and output files

scripts/combine_dfs.py

@@ -41,7 +41,7 @@ homedir = os.path.expanduser('~')
 
 # set working dir
 os.getcwd()
-os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis')
+os.chdir(homedir + '/git/LSHTM_analysis/scripts')
 os.getcwd()
 #=======================================================================
 #%% command line args

scripts/or_kinship_link.py

@@ -5,50 +5,45 @@ Created on Wed Jun 10 11:13:49 2020
 
 @author: tanu
 """
+#=======================================================================
 #%% useful links
-
 #https://chrisalbon.com/python/data_wrangling/pandas_join_merge_dataframe/
 #https://kanoki.org/2019/11/12/how-to-use-regex-in-pandas/
 #https://stackoverflow.com/questions/40348541/pandas-diff-with-string
-#%%
+#=======================================================================
+#%% specify dirs
 import os, sys
 import pandas as pd
 #import numpy as np
 import re
-from find_missense import find_missense
 import argparse
 
-#%%
-# homedir
 homedir = os.path.expanduser('~')
-#os.chdir(homedir + '/git/Misc/jody_pza')
+os.chdir(homedir + '/git/LSHTM_analysis/scripts')
+# local import
+from find_missense import find_missense
 #=======================================================================
 #%% 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 = None)
 arg_parser.add_argument('-g', '--gene', help = 'gene name (case sensitive)', default = None) # case sensitive
 
-#arg_parser.add_argument('-p', '--outpath', help = 'output path', default = outpath)
-#arg_parser.add_argument('-o', '--outfile', help = 'output filename', default = outfile_or_kin) 
-
 arg_parser.add_argument('-s', '--start_coord', help = 'start of coding region (cds) of gene', default = 2288681) # pnca cds
 arg_parser.add_argument('-e', '--end_coord', help = 'end of coding region (cds) of gene', default = 2289241) # pnca cds
 
 args = arg_parser.parse_args()
 #=======================================================================
 #%% variables
-#or_file
-#info_file
-#short_info_file
 #gene = 'pncA'
 #drug = 'pyrazinamide'
-start_cds = args.start_coord
-end_cds = args.end_coord
 
+# cmd variables
 gene = args.gene
 drug = args.drug
+
+start_cds = args.start_coord
+end_cds = args.end_coord
 #=======================================================================
 #%% input and output dirs and files
 #=======
@@ -82,7 +77,7 @@ print('gene OR file: ', gene_or
 #=======
 # output
 #=======
-gene_or_filename = gene.lower() + '_AF_OR_kinship.csv' # other one is called AFandOR
+gene_or_filename = gene.lower() + '_af_or_kinship.csv' # other one is called AFandOR
 outfile_or_kin =  outdir + '/' + gene_or_filename
 print('Output file: ', outfile_or_kin
       , '\n============================================================')