From da0c03c2e0e276cc86e4e03f461d513006b18211 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Mon, 13 Jul 2020 12:20:43 +0100
Subject: [PATCH] trying to resolve copy warning in code

---
 scripts/or_kinship_link.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/scripts/or_kinship_link.py b/scripts/or_kinship_link.py
index 2ddac12..5d4bc6b 100755
--- a/scripts/or_kinship_link.py
+++ b/scripts/or_kinship_link.py
@@ -34,8 +34,8 @@ arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb fi
 arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
 
 # FIXME: remove defaults 
-arg_parser.add_argument('-s', '--start_coord', help = 'start of coding region (cds) of gene', default = 2288681) # pnca cds 
-arg_parser.add_argument('-e', '--end_coord', help = 'end of coding region (cds) of gene', default = 2289241) # pnca cds
+arg_parser.add_argument('-sc', '--start_coord', help = 'start of coding region (cds) of gene', default = None, type = int) # pnca cds 
+arg_parser.add_argument('-ec', '--end_coord', help = 'end of coding region (cds) of gene', default = None, type = int) # pnca cds
 
 arg_parser.add_argument('--debug', action ='store_true', help = 'Debug Mode')
 
@@ -314,18 +314,21 @@ print('No. of cols pre-formatting data:', df_ncols
 #1) Add column: OR for kinship calculated from beta coef
 ncols_add = 0
 if not 'or_kin' in dfm2_mis.columns:
-    dfm2_mis['or_kin'] = np.exp(dfm2_mis['beta'])
+    #dfm2_mis['or_kin'] = np.exp(dfm2_mis['beta']) # gives copy warning
+    dfm2_mis.loc[:,'or_kin'] = np.exp(dfm2_mis.loc[:,'beta'])
+    
     print(dfm2_mis['or_kin'].head())
     ncols_add+=1
     print('Calculating OR from beta coeff by exponent function and adding column:'
-      , '\nNo. of cols added:', ncols_add, '\n'
-      ,  dfm2_mis['beta'].head()
+      , '\nNo. of cols added:', ncols_add
+      , '\n', dfm2_mis['beta'].head()
+      , '\nNo. of cols after adding OR_kin:', len(dfm2_mis.columns)
       , '\n===================================================================')  
     
 if dfm2_mis.shape[1] == df_ncols + ncols_add:
     print('PASS: Dimension of df match'
           , '\nDim of df:', dfm2_mis.shape
-          , 'n================================================================')
+          , '\n================================================================')
 else:
     print('FAIL: Dim mismatch'
           , '\nOriginal no. of cols:', df_ncols
@@ -333,8 +336,6 @@ else:
           , '\nGot:', dfm2_mis.shape[1])
     sys.exit()
 
-print('No. of cols after adding OR_kin:', len(dfm2_mis.columns))
-
 #2) rename columns to reflect that it is coming from kinship matrix adjustment
 dfm2_mis.rename(columns = {'af': 'af_kin'
                            , 'beta': 'beta_kin'
@@ -399,7 +400,7 @@ else:
     sys.exit()
  
 del(df_ncols)
-#%%
+#%%=====================================================================
 #4) reorder columnn
 print('Reordering', dfm2_mis.shape[1], 'columns'
       , '\n===============================================')