From c43e57674b800f80bc9e6cf4c53e995ecd9e2e44 Mon Sep 17 00:00:00 2001 From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu> Date: Thu, 7 Nov 2019 09:20:37 -0600 Subject: [PATCH] Fix #34 to remove trailing and leading whitespace in design file contents --- CHANGELOG.md | 2 +- workflow/scripts/check_design.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6a6692b..b4c48ac 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ * Change Cellranger Version to 3.1.0 * Fix countDesign to take multiple samples * Add MIT License -* Check Design File for spaces in name +* Check Design File for spaces in name and file contents * Update design example, README, and astrocyte.yml with current barcode IDs **Background** diff --git a/workflow/scripts/check_design.py b/workflow/scripts/check_design.py index a1cbe0e..3fa3859 100644 --- a/workflow/scripts/check_design.py +++ b/workflow/scripts/check_design.py @@ -55,7 +55,7 @@ def check_design_headers(design): if len(missing_headers) > 0: logger.error('Missing column headers: %s', list(missing_headers)) raise Exception("Missing column headers: %s" % list(missing_headers)) - + return design def main(): @@ -67,7 +67,7 @@ def main(): logger.addHandler(handler) # Read files as dataframes - design_df = pd.read_csv(args.design, sep=',') + design_df = pd.read_csv(args.design, sep=',', converters={'Lane': str.strip, 'Sample': str.strip, 'Index': str.strip}) # Check design file new_design_df = check_design_headers(design_df) @@ -75,4 +75,4 @@ def main(): new_design_df.to_csv('design.checked.csv', header=True, sep=',', index=False) if __name__ == '__main__': - main() \ No newline at end of file + main() -- GitLab