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()
--
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