From 566234152d5e992b50c20ac9d2564b450935b3e5 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 10 Jan 2018 15:36:02 -0600
Subject: [PATCH] Fix control file path.
---
workflow/scripts/pool_and_psuedoreplicate.py | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 17755ab..2890ff2 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -242,8 +242,9 @@ def main():
# Check controls against cutoff_ratio
# if so replace with pool_control
# unless single control was used
- path_to_pool_control = cwd + '/' + pool_control
+
if not single_control:
+ path_to_pool_control = cwd + '/' + pool_control
if control_df.values.max() > 1.2:
logger.info("Number of reads in controls differ by " +
" > factor of %f. Using pooled controls." % (cutoff_ratio))
@@ -258,6 +259,8 @@ def main():
% row['replicate'])
design_new_df.loc[index, 'control_tag_align'] = \
path_to_pool_control
+ else:
+ path_to_pool_control = pool_control
# Add in pseudo replicates
tmp_metadata = design_new_df.loc[0].copy()
--
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