Merge branch 'maintenance_pandas' into 'master'

Maintenance pandas

See merge request !14

raiss/filter_format_output.py

@@ -17,7 +17,7 @@ def filter_output(zscores, fout, R2_threshold = 0.6, minimum_ld = 5):
 
 
     zscores.reset_index(inplace = True)
-    zscores = zscores[['index', 'pos', 'A0', 'A1', 'Z', 'Var', "ld_score"]]
+    zscores = zscores[['index', 'pos', 'A0', 'A1', 'Z', 'Var', "ld_score"]].copy()
     zscores["imputation_R2"] = 1-zscores["Var"]
     zscores.columns = ['rsID','pos','A0','A1','Z', 'Var', "ld_score", "imputation_R2"]
 

raiss/windows.py

@@ -42,6 +42,8 @@ def realigned_zfiles_on_panel(ref_panel, zscore):
     zscore.sort_index(inplace=True)
     sub_ref_panel.sort_index(inplace=True)
 
+    print(sub_ref_panel.Ref_all)
+    print(zscore.A0)
     allele_inverted = (sub_ref_panel.Ref_all != zscore.A0)
 
     zscore.loc[allele_inverted, "A0"] = sub_ref_panel.loc[allele_inverted].Ref_all
@@ -188,7 +190,13 @@ def impg_like_imputation(ld_file, ref_panel, zscore, window_size, buffer, lamb,
                 in_core_window = in_region(batch_df.pos, start_core_window, end_core_window)
 
                 batch_df_filt = batch_df.loc[(in_core_window), zscore_results.columns]
-                zscore_results = pd.concat([zscore_results, batch_df_filt])
+                if ((batch_df_filt.empty==False) or (batch_df_filt.dropna().empty==False)):
+                    if zscore_results.empty:
+                        zscore_results = batch_df_filt
+                    else:
+                        zscore_results = pd.concat([zscore_results, batch_df_filt])
+
+                
             except (ValueError, KeyError, TypeError) as e:
                 print("Inversion failed for window {0} - {1}".format(start_windows,end_windows ))
                 print("With error : {}".format(e))