ran mcsm_na for rpob's RNAP complex i.e 5UHC

mcsm_na/run_format_results_mcsm_na.py

@@ -52,15 +52,16 @@ if not outdir:
 outdir_na = outdir + 'mcsm_na_results/'
 
 # Input file
-infile_mcsm_na =  outdir_na +  gene + '_output_combined_clean.tsv'
+infile_mcsm_na =  outdir_na +  gene.lower() + '_output_combined_clean.tsv'
 
 # Formatted output file
-outfile_mcsm_na_f = outdir_na + gene + '_complex_mcsm_na_norm.csv'
+outfile_mcsm_na_f = outdir_na + gene.lower() + '_complex_mcsm_na_norm.csv'
 
-#==========================
+#===========================================
 # CALL: format_results_mcsm_na() 
 # Data: gid+streptomycin
-#==========================
+# Data: rpob+rifampicin, date: 18/11/2021
+#===========================================
 print('Formatting results for:', infile_mcsm_na)
 mcsm_na_df_f = format_mcsm_na_output(mcsm_na_output_tsv = infile_mcsm_na)
 

mcsm_na/run_submit_mcsm_na.py

@@ -18,14 +18,14 @@ print(my_prediction_url)
 
 # TODO: add cmd line args
 #gene = 'gid'
-drug = 'streptomycin'
-datadir = homedir + '/git/Data'
-indir = datadir + '/' + drug + '/input'
-outdir = datadir + '/' + drug + '/output'
-outdir_mcsm_na = outdir + 'mcsm_na_results'
+drug = ''
+datadir = homedir + '/git/Data/'
+indir = datadir + drug + 'input/'
+outdir = datadir + drug + 'output/'
+outdir_mcsm_na = outdir + 'mcsm_na_results/'
 
 my_nuc_type = 'RNA'
-my_pdb_file = indir + '/gid_complex.pdb'
+my_pdb_file = indir + gene.lower() + '_complex.pdb'
 
 #=============================================================================
 # batch 26: 25.txt # RAN: 16 Feb: