From 2eab17cb9e5c730affb27fa76e2f853c993bc33f Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Thu, 11 Feb 2021 10:53:23 +0000
Subject: [PATCH] uncommented some debug output for mcsm, pandas and numpy
 conflict. So temporarily resolved it by running from base env

---
 dynamut/submit.py | 8 ++++++--
 mcsm/mcsm.py      | 1 +
 mcsm/run_mcsm.py  | 4 ++--
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/dynamut/submit.py b/dynamut/submit.py
index a2acecc..7b8f0d1 100755
--- a/dynamut/submit.py
+++ b/dynamut/submit.py
@@ -60,8 +60,12 @@ with open("/home/tanu/git/Data/streptomycin/input/gid_complex.pdb", "rb") as pdb
             failed_muts.close()
 
 #%%
-def request_calculation(pdb_file, mutation_list, chain, my_email, prediction_url
-                        #, output_dir, gene_name
+def request_calculation(pdb_file, mutation_list
+                        , chain
+                        , my_email
+                        , prediction_url
+                        , output_dir
+                        , gene_name
                         , url_file):
     """
     Makes a POST request for a ligand affinity prediction.
diff --git a/mcsm/mcsm.py b/mcsm/mcsm.py
index b098636..1adf57c 100644
--- a/mcsm/mcsm.py
+++ b/mcsm/mcsm.py
@@ -166,6 +166,7 @@ def build_result_dict(web_result_raw):
         if len(fields) > 1:  # since Mutaton information is empty
             dict_entry = dict([(x, y) for x, y in zip(fields[::2], fields[1::2])])
         result_dict.update(dict_entry)
+    print(result_dict)
     return result_dict
 #%%
 #=======================================================================
diff --git a/mcsm/run_mcsm.py b/mcsm/run_mcsm.py
index d23f8da..7e38543 100755
--- a/mcsm/run_mcsm.py
+++ b/mcsm/run_mcsm.py
@@ -163,7 +163,7 @@ def get_results():
     output_df = pd.DataFrame()
     url_counter = 1 # HURR DURR COUNT STARTEDS AT ONE1`!1
     success_counter = 1
-    infile_len = os.popen('wc -l < %s' % result_urls).read() # quicker than using Python :-) #FIXME filenme (infile_urls)
+    infile_len = os.popen('wc -l < %s' % result_urls).read() # quicker than using Python :-)
 
     print('Total URLs:', infile_len)
 
@@ -181,7 +181,7 @@ def get_results():
             url_counter += 1
             
     print('Total URLs: %s Successful: %s Failed: %s' % (url_counter-1, success_counter-1, (url_counter - success_counter)))
-
+    #print('\nOutput file created:', output_dir + gene.lower() + '_mcsm_output.csv')
     output_df.to_csv(mcsm_output, index = None, header = True)
 #%%=====================================================================
 def format_results():