From 7fd5e2710d7792f4f17008faaf38677e02aa7a12 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Fri, 19 Nov 2021 07:48:42 +0000
Subject: [PATCH] ran mcsm_na for rpob's RNAP complex i.e 5UHC

---
 mcsm_na/examples.py                   |  0
 mcsm_na/format_results_mcsm_na.py     |  0
 mcsm_na/get_results_mcsm_na.py        |  0
 mcsm_na/run_format_results_mcsm_na.py |  9 +++++----
 mcsm_na/run_submit_mcsm_na.py         | 12 ++++++------
 mcsm_na/submit_mcsm_na.py             |  0
 scripts/combining_dfs.py              |  4 ++--
 7 files changed, 13 insertions(+), 12 deletions(-)
 mode change 100644 => 100755 mcsm_na/examples.py
 mode change 100644 => 100755 mcsm_na/format_results_mcsm_na.py
 mode change 100644 => 100755 mcsm_na/get_results_mcsm_na.py
 mode change 100644 => 100755 mcsm_na/run_format_results_mcsm_na.py
 mode change 100644 => 100755 mcsm_na/submit_mcsm_na.py

diff --git a/mcsm_na/examples.py b/mcsm_na/examples.py
old mode 100644
new mode 100755
diff --git a/mcsm_na/format_results_mcsm_na.py b/mcsm_na/format_results_mcsm_na.py
old mode 100644
new mode 100755
diff --git a/mcsm_na/get_results_mcsm_na.py b/mcsm_na/get_results_mcsm_na.py
old mode 100644
new mode 100755
diff --git a/mcsm_na/run_format_results_mcsm_na.py b/mcsm_na/run_format_results_mcsm_na.py
old mode 100644
new mode 100755
index a5886b4..b2175f5
--- a/mcsm_na/run_format_results_mcsm_na.py
+++ b/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)
 
diff --git a/mcsm_na/run_submit_mcsm_na.py b/mcsm_na/run_submit_mcsm_na.py
index 8f7ed90..4de2455 100755
--- a/mcsm_na/run_submit_mcsm_na.py
+++ b/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:
diff --git a/mcsm_na/submit_mcsm_na.py b/mcsm_na/submit_mcsm_na.py
old mode 100644
new mode 100755
diff --git a/scripts/combining_dfs.py b/scripts/combining_dfs.py
index a0c570b..e6ea6cc 100755
--- a/scripts/combining_dfs.py
+++ b/scripts/combining_dfs.py
@@ -122,8 +122,8 @@ if gene.lower() == "gid":
     in_filename_mcsm = gene.lower() + '_complex_mcsm_norm_SRY.csv' # was incorrectly SAM previously
 if gene.lower() == "embb":
     print("\nReading mCSM file for gene:", gene)
-    #in_filename_mcsm = gene.lower() + '_complex_mcsm_norm1.csv'
-    in_filename_mcsm = gene.lower() + '_complex_mcsm_norm2.csv'
+    #in_filename_mcsm = gene.lower() + '_complex_mcsm_norm1.csv' #798
+    in_filename_mcsm = gene.lower() + '_complex_mcsm_norm2.csv' #844
 
 if gene.lower() in gene_list_normal:
    print("\nReading mCSM file for gene:", gene)