From 2c96e9d4390991abe1f182b215a00db03f7f1af0 Mon Sep 17 00:00:00 2001 From: j-berg Date: Tue, 23 Feb 2021 17:34:00 -0700 Subject: [PATCH] More debugging --- xpresspipe/Rmetagene.r | 3 +++ xpresspipe/metagene.py | 3 +++ 2 files changed, 6 insertions(+) diff --git a/xpresspipe/Rmetagene.r b/xpresspipe/Rmetagene.r index e00d85b..dac9c02 100644 --- a/xpresspipe/Rmetagene.r +++ b/xpresspipe/Rmetagene.r @@ -119,6 +119,8 @@ 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=' ')) } } @@ -126,3 +128,4 @@ run_list <- function ( # 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 index fdaa528..4c4aaea 100644 --- 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