From 93fae9e5f5eebf319c6d6677658b1157478628ea Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Thu, 12 Aug 2021 15:29:36 +0100
Subject: [PATCH] reran b7 since previous run file output was 0 bytes

---
 dynamut/run_submit_dynamut.py | 33 ++++++++++++++++++++-------------
 dynamut/submit_dynamut.py     |  4 +++-
 2 files changed, 23 insertions(+), 14 deletions(-)

diff --git a/dynamut/run_submit_dynamut.py b/dynamut/run_submit_dynamut.py
index 6408a4e..65460b2 100755
--- a/dynamut/run_submit_dynamut.py
+++ b/dynamut/run_submit_dynamut.py
@@ -17,7 +17,7 @@ my_prediction_url = f"{my_host}/dynamut/prediction_list"
 print(my_prediction_url)
 
 # TODO: add cmd line args
-#gene = 'gid'
+gene = 'gid'
 drug = 'streptomycin'
 datadir = homedir + '/git/Data/'
 indir = datadir + drug + '/input/'
@@ -27,8 +27,8 @@ outdir_dynamut = outdir + 'dynamut_results/'
 my_chain = 'A'
 my_email = 'tanushree.tunstall@lshtm.ac.uk'
 
-my_pdb_file = indir + 'gid_complex.pdb'
-
+#my_pdb_file = indir + 'gid_complex.pdb'
+my_pdb_file = indir +  gene + '_complex.pdb'
 #==============================================================================
 # batch 7: 07.txt, # RAN: 22 Feb 09:26
 #my_mutation_list = outdir + '/snp_batches/50/snp_batch_07.txt'
@@ -40,21 +40,28 @@ my_pdb_file = indir + 'gid_complex.pdb'
 
 # batch 9 and 10 failed!
 # bissecting: b10, split into 5 (1st failed, 2nd worked, but then comb rest)
-
-my_mutation_list = outdir + 'snp_batches/50/b9_b10_bissect/b10_21.txt'
-my_suffix = 'gid_b10_21'
+# Rerunnig batch 7: 07.txt, # RAN: 12 Aug 15:22, 0 bytes file from previous run!
+my_mutation_list = outdir + 'snp_batches/50/snp_batch_07.txt'
+my_suffix = 'gid_b7'
 #==============================================================================
 
 #==========================
 # CALL: submit_dynamut() 
 # Data: gid+streptomycin
 #==========================
+print('\nSubmitting batch for:'
+      , '\ndrug: '       , drug
+      , '\ngene: '       , gene
+      , '\nbatch: '      , my_suffix
+      , '\n\nFilename: ' , my_mutation_list)
+
 submit_dynamut(host_url = my_host
-               , pdb_file = my_pdb_file
-               , mutation_list = my_mutation_list
-               , chain = my_chain
-               , email_address = my_email
-               , prediction_url = my_prediction_url
-               , output_dir = outdir_dynamut
-               , outfile_suffix = my_suffix) 
+                , pdb_file = my_pdb_file
+                , mutation_list = my_mutation_list
+                , chain = my_chain
+                , email_address = my_email
+                , prediction_url = my_prediction_url
+                , output_dir = outdir_dynamut
+                , outfile_suffix = my_suffix) 
+
 #%%#####################################################################               
diff --git a/dynamut/submit_dynamut.py b/dynamut/submit_dynamut.py
index 37e03be..8d72218 100755
--- a/dynamut/submit_dynamut.py
+++ b/dynamut/submit_dynamut.py
@@ -80,7 +80,9 @@ def submit_dynamut(host_url
                 os.makedirs(dynamut_temp_dir)                    
             
             out_url_file = dynamut_temp_dir + 'dynamut_result_url_' + str(outfile_suffix) + '.txt'
-            print('\nWriting output url file:', out_url_file)
+            print('\nWriting output url file:', out_url_file
+                  , '\nNow we wait patiently...')
+            
             myfile = open(out_url_file, 'a')    
             myfile.write(url)
             myfile.close()