More debugging

XPRESSyourself · Feb 24, 2021 · 2c96e9d · 2c96e9d
1 parent f1970fc
commit 2c96e9d
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Showing 2 changed files with 6 additions and 0 deletions.
diff --git a/xpresspipe/Rmetagene.r b/xpresspipe/Rmetagene.r
@@ -119,10 +119,13 @@ run_list <- function (
       file_name = vapply(strsplit(f, "[.]"), `[`, 1, FUN.VALUE=character(1))
       output_file = paste(output_path, file_name, '.metaposit', sep='')
       write.table(bam, file=output_file, sep='\t', col.names=NA)
+
+      print(paste('Metagene profile for', toString(f), 'written to', toString(output_file), sep=' '))
     }
   }
 
 # MAIN
 # Run files through coverage checker
 print(paste('Rscript processing file list:', BAM_LIST, sep=' '))
 run_list(BAM_PATH, BAM_LIST, OUTPUT_LOCATION)
+print("Metagene BAM file processing complete.")
diff --git a/xpresspipe/metagene.py b/xpresspipe/metagene.py
@@ -49,6 +49,8 @@ def finish_metagene(
 
     file, args_dict = args[0], args[1]
 
+    print('Reading in ' + str(args_dict['metagene']) + 'metrics/' + str(file).split('.')[0] + '.metaposit')
+
     # Read in parsed bam
     bam = pd.read_csv(
         str(args_dict['metagene']) + 'metrics/' + str(file).split('.')[0] + '.metaposit',
@@ -130,6 +132,7 @@ def finish_metagene(
     profile.to_csv(
         str(args_dict['metagene']) + 'metrics/' + str(file).split('.')[0] + '_metrics.txt',
         sep='\t')
+    print('Profile exported to ' + str(args_dict['metagene']) + 'metrics/' + str(file).split('.')[0] + '_metrics.txt')
 
     # Clean up
     bam = None