Less restrictive env.

pd append2concat update

Author: fercrcode

code/4-dremi.py

@@ -145,7 +145,7 @@
                 if num_outliers_total == 0:
                     df_info_dict[colname_arc] = "-" # this is a placeholder
         # Store the info for each marker pair in df_info      
-        df_info = df_info.append(df_info_dict, ignore_index=True)    
+        df_info = pd.concat([df_info, df_info_dict], ignore_index=True)    
 
 
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Save to file~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#

code/aux/aux3_emd.py

@@ -43,6 +43,6 @@ def calculate_emd(marker_list, emd_infodict, compare_from, compare_to,
                                                         compare_from[marker],
                                                         compare_to[marker])
         #Add EMD score to the output dataframe
-        emd_df = emd_df.append(emd_infodict, ignore_index=True)
+        emd_df = pd.concat([emd_df, pd.DataFrame([emd_infodict])], ignore_index=True)
 
     return emd_df

code/aux/aux_functions.py

@@ -171,7 +171,7 @@ def concatenate_fcs(input_dir):
                                             lambda x: str(fcounter)+"-"+str(x))
         except KeyError:
             sys.exit("ERROR: Cell_Index missing from data. Have you preprocessed it?")
-        no_arc = no_arc.append(df, ignore_index=True)
+        no_arc = pd.concat([no_arc, df], ignore_index=True)
     return no_arc, filelist
 
 #Function to concatenate all files and save as txt -> DEPRECATE IN THE NEAR FUTURE!
@@ -199,7 +199,7 @@ def concatenate_save(input_dir, output_dir):
         df["Sample_ID-Cell_Index"] = df["Cell_Index"].apply(
                                         lambda x: str(fcounter)+"-"+str(x)) #File+ID #This way the cell-index will be preserved after Cytobank upload
         # df["Cell_Index"] = df["Cell_Index"].apply(lambda x: str(fcounter)+"-"+str(x)) #File+ID
-        concat = concat.append(df, ignore_index=True)
+        concat = pd.concat([concat, df], ignore_index=True)
     print("Concatenating...")
     concat.to_csv(f'{output_dir}/concat_{name}.txt', index = False, sep = '\t')
     print(f"Concatenated file saved as:\nconcat_{name}.txt")

conda_env.yml

@@ -3,9 +3,9 @@ channels:
   # - bioconda
   - conda-forge
 dependencies: 
-  - python=3.8  
-  - pip=21  
-  - r-base=4.0
+  - python=3 
+  - pip
+  - r-base=4
   - natsort  
   - numpy #ALLarch
   - pandas  #ALLarch