output filenames in omics py

Author: alexandriai168

build/novartispdx/02-omics-novartispdx.py

@@ -278,7 +278,7 @@ def map_mutations_novPDX(mutation_data, improve_id_data, entrez_data):
         # Download parse excel file to get mutation data and the copy num data
         mutation_df, copy_num_df, rnaseq_df = download_parse_omics_novPDX(synID="syn66477971", save_path="/tmp/", synToken=args.token)
         # Save mutation and copy number data into csv format
-        mutation_df.to_csv("/tmp/mutation_data.csv")
+        mutation_df.to_csv("/tmp/raw_mutation_data.csv")
         copy_num_df.to_csv("/tmp/copy_num_data.csv")
         rnaseq_df.to_csv("/tmp/rnaseq_data.csv")
 
@@ -291,8 +291,8 @@ def map_mutations_novPDX(mutation_data, improve_id_data, entrez_data):
             exit()
         else:
             print("Starting transcriptomics data.")
-            transcriptomics_df = map_transcriptomics_novPDX(transciptomics_data = "/tmp/rnaseq_data.csv", improve_id_data = "/tmp/novartispdx_samples.csv", entrez_data = "/tmp/genes.csv")
-            transcriptomics_df.to_csv("/tmp/crcpdo_transcriptomics.csv", index=False)
+            transcriptomics_df = map_transcriptomics_novPDX(transciptomics_data = "/tmp/raw_rnaseq_data.csv", improve_id_data = "/tmp/novartispdx_samples.csv", entrez_data = "/tmp/genes.csv")
+            transcriptomics_df.to_csv("/tmp/novartispdx_transcriptomics.csv", index=False)
 
     if args.mutations:
         if args.genes is None or args.genes=='':
@@ -303,8 +303,8 @@ def map_mutations_novPDX(mutation_data, improve_id_data, entrez_data):
             exit()
         else:
             print("Starting mutations data.")
-            mutation_df = map_mutations_novPDX(mutation_data = "/tmp/mutation_data.csv", improve_id_data = "/tmp/novartispdx_samples.csv", entrez_data = "/tmp/genes.csv")
-            mutation_df.to_csv("/tmp/crcpdo_mutations.csv", index=False)
+            mutation_df = map_mutations_novPDX(mutation_data = "/tmp/raw_mutation_data.csv", improve_id_data = "/tmp/novartispdx_samples.csv", entrez_data = "/tmp/genes.csv")
+            mutation_df.to_csv("/tmp/novartispdx_mutations.csv", index=False)
 
     if args.copy_number:
         if args.genes is None or args.genes=='':
@@ -315,6 +315,6 @@ def map_mutations_novPDX(mutation_data, improve_id_data, entrez_data):
             exit()
         else:
             print("Starting copy number data.")
-            mutation_df = map_copy_number_novPDX(copy_number_data = "/tmp/copy_num_data.csv", improve_id_data = "/tmp/novartispdx_samples.csv", entrez_data = "/tmp/genes.csv")
-            mutation_df.to_csv("/tmp/crcpdo_copy_number.csv", index=False)
+            mutation_df = map_copy_number_novPDX(copy_number_data = "/tmp/raw_copy_num_data.csv", improve_id_data = "/tmp/novartispdx_samples.csv", entrez_data = "/tmp/genes.csv")
+            mutation_df.to_csv("/tmp/novartispdx_copy_number.csv", index=False)