adpated combining_dfs.py and plotting.R for gid and attempting to make it generic

scripts/combining_dfs.py

@@ -57,10 +57,10 @@ from combining_FIXME import detect_common_cols
 from reference_dict import oneletter_aa_dict # CHECK DIR STRUC THERE!
 from reference_dict import low_3letter_dict # CHECK DIR STRUC THERE!
 #=======================================================================
-#%% command line args
+#%% command line args: case sensitive
 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 = '')
+arg_parser.add_argument('-g', '--gene', help='gene name', default = '') 
 
 arg_parser.add_argument('--datadir', help = 'Data Directory. By default, it assmumes homedir + git/Data')
 arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb files. By default, it assmumes homedir + <drug> + input')
@@ -99,32 +99,37 @@ print('position regex:', pos_regex)
 # directories
 #==============
 if not datadir:
-    datadir = homedir + '/' + 'git/Data'
+    datadir = homedir + '/git/Data/'
     
 if not indir:
-    indir = datadir + '/' + drug + '/input'
+    indir = datadir + drug + '/input/'
     
 if not outdir:
-    outdir = datadir + '/' + drug + '/output'
+    outdir = datadir + drug + '/output/'
 
 #=======
 # input
 #=======
-in_filename_mcsm = gene.lower() + '_complex_mcsm_norm.csv'
+#in_filename_mcsm = gene.lower() + '_complex_mcsm_norm.csv' 
+in_filename_mcsm = gene.lower() + '_complex_mcsm_norm_SAM.csv' # gidb
 in_filename_foldx = gene.lower() + '_foldx.csv'
 in_filename_dssp = gene.lower() + '_dssp.csv'
 in_filename_kd = gene.lower() + '_kd.csv'
 in_filename_rd = gene.lower() + '_rd.csv'
-in_filename_snpinfo = 'ns' + gene.lower() + '_snp_info_f.csv'
+#in_filename_deepddg = gene.lower() + '_complex_ddg_results.txt' # change to decent filename and put it in the correct dir
+
+in_filename_snpinfo = 'ns' + gene.lower() + '_snp_info_f.csv' # gwas f info
 in_filename_afor = gene.lower() + '_af_or.csv'
 in_filename_afor_kin = gene.lower() + '_af_or_kinship.csv'
 
 
-infile_mcsm = outdir + '/' + in_filename_mcsm
-infile_foldx = outdir + '/' + in_filename_foldx
-infile_dssp = outdir + '/' + in_filename_dssp
-infile_kd = outdir + '/' + in_filename_kd
-infile_rd = outdir + '/' + in_filename_rd
+infile_mcsm = outdir + in_filename_mcsm
+infile_foldx = outdir + in_filename_foldx
+infile_dssp = outdir + in_filename_dssp
+infile_kd = outdir + in_filename_kd
+infile_rd = outdir + in_filename_rd
+#infile_deepddg = outdir + in_filename_deepddg
+
 infile_snpinfo = outdir + '/' + in_filename_snpinfo 
 infile_afor = outdir + '/' + in_filename_afor
 infile_afor_kin = outdir + '/' + in_filename_afor_kin
@@ -135,7 +140,9 @@ print('\nInput path:', indir
       , '\nInput filename foldx:', infile_foldx, '\n'
       , '\nInput filename dssp:', infile_dssp
       , '\nInput filename kd:', infile_kd 
-      , '\nInput filename rd', infile_rd , '\n'
+      , '\nInput filename rd', infile_rd
+#     , '\nInput filename rd', infile_deepddg , '\n'
+      
       , '\nInput filename snp info:', infile_snpinfo, '\n'
       , '\nInput filename af or:', infile_afor
       , '\nInput filename afor kinship:', infile_afor_kin
@@ -225,10 +232,39 @@ print('\nResult of Fourth merge:', combined_df.shape
       , '\n===================================================================')
 combined_df[merging_cols_m4].apply(len)
 combined_df[merging_cols_m4].apply(len) == len(combined_df)
+
 #%%============================================================================
 
-# OR merges: TEDIOUSSSS!!!!
+#deepddg_df =  pd.read_csv(infile_deepddg, sep = ' ')
 
+
+
+
+
+#%%============================================================================
+# Output columns
+
+out_filename_stab_struc = gene.lower() + '_comb_stab_struc_params.csv'
+outfile_stab_struc =  outdir + '/' + out_filename_stab_struc
+print('Output filename:', outfile_stab_struc
+      , '\n===================================================================')
+
+# write csv
+print('Writing file: combined stability and structural parameters')
+combined_df.to_csv(outfile_stab_struc, index = False)
+print('\nFinished writing file:'
+      , '\nNo. of rows:', combined_df.shape[0]
+      , '\nNo. of cols:', combined_df.shape[1])
+
+
+
+
+
+
+
+#%%============================================================================
+# OR merges: TEDIOUSSSS!!!!
+#[ DELETE ]
 del(mcsm_df, foldx_df, mcsm_foldx_dfs, dssp_kd_dfs, dssp_kd_rd_dfs,rd_df, kd_df, infile_mcsm, infile_foldx, infile_dssp, infile_kd)
 del(merging_cols_m1, merging_cols_m2, merging_cols_m3, merging_cols_m4)
 del(in_filename_dssp, in_filename_foldx, in_filename_kd, in_filename_mcsm, in_filename_rd)