refactoring: added command line args to combine_dfs

meta_data_analysis/combine_dfs.py

@@ -6,35 +6,36 @@ Created on Tue Aug  6 12:56:03 2019
 @author: tanu
 '''
 # FIXME: change filename 4 (mcsm normalised data)
-# to be consistent like (pnca_mcsm_norm.csv)
+# to be consistent like (pnca_complex_mcsm_norm.csv) : changed manually, but ensure this is done in the mcsm pipeline
 #=============================================================================
 # Task: combine 4 dfs with aa position as linking column
 # This is done in 2 steps:
-# merge 1: of 3 dfs
+# merge 1: of 3 dfs (filenames in lowercase)
-#   pnca_dssp.csv
+#   <gene.lower()>_dssp.csv
-#   pnca_kd.csv
+#   <gene.lower()>_kd.csv
-#   pnca_rd.csv
+#   <gene.lower()>_pnca_rd.csv
 
 # merge 2: of 2 dfs
-#    mcsm_complex1_normalised.csv (!fix name)
+#    pnca_complex_mcsm_norm.csv (!fix name in mcsm script)
 #    output df from merge1
 
 # Input: 3 dfs
-# pnca_dssp.csv
+#   <gene.lower()>_dssp.csv
-# pnca_kd.csv
+#   <gene.lower()>_kd.csv
-# pnca_rd.csv
+#   <gene.lower()>_pnca_rd.csv
-# mcsm_complex1_normalised.csv (!fix name)
+# pnca_complex_mcsm_norm.csv (!fix name in mcsm script)
 
 # Output: .csv of all 4 dfs combined
 
 # useful link
-#https://stackoverflow.com/questions/23668427/pandas-three-way-joining-multiple-dataframes-on-columns
+# https://stackoverflow.com/questions/23668427/pandas-three-way-joining-multiple-dataframes-on-columns
 #=============================================================================
 #%% load packages
 import sys, os
 import pandas as pd
 #import numpy as np
-#=============================================================================
+import argparse
+#=======================================================================
 #%% specify input and curr dir
 homedir = os.path.expanduser('~')
 
@@ -42,27 +43,36 @@ homedir = os.path.expanduser('~')
 os.getcwd()
 os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis')
 os.getcwd()
-#=============================================================================
+#=======================================================================
+#%% 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 = 'pyrazin')
+arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pn') # case sensitive
+args = arg_parser.parse_args()
+#=======================================================================
 #%% variable assignment: input and output 
-drug = 'pyrazinamide'
+#drug = 'pyrazinamide'
-gene = 'pncA'
+#gene = 'pncA'
-gene_match = gene + '_p.'
+#gene_match = gene + '_p.'
 
+drug = args.drug
+gene = args.gene
 #==========
 # data dir
 #==========
-#indir = 'git/Data/pyrazinamide/input/original'
 datadir = homedir + '/' + 'git/Data'
 
 #=======
 # input
 #=======
-#indir = 'git/Data/pyrazinamide/input/original'
 indir = datadir + '/' + drug + '/' + 'output'
 in_filename1 = 'pnca_dssp.csv'
 in_filename2 = 'pnca_kd.csv'
 in_filename3 = 'pnca_rd.csv'
-in_filename4 = 'mcsm_complex1_normalised.csv' # FIXNAME
+#in_filename4 = 'mcsm_complex1_normalised.csv' # Fix name in mcsm script
+in_filename4 = 'pnca_complex_mcsm_norm.csv'  # manually changed temporarily
 
 infile1 = indir + '/' + in_filename1
 infile2 = indir + '/' + in_filename2
@@ -235,4 +245,4 @@ print('Finished writing:', out_filename
       , '\n===================================================================')
 
 #%% end of script
-#==============================================================================
+#==============================================================================