From 096e1e79c37048c0ce564fa393dc32b6924be4ea Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 28 Jan 2020 16:26:12 -0600
Subject: [PATCH] Fix logic if paired-end and single replicate.
---
workflow/scripts/pool_and_psuedoreplicate.py | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 25cc444..efefad9 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -204,6 +204,7 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
pool_control_tmp = bedpe_to_tagalign(pool_control, "pool_control")
pool_control = pool_control_tmp
+
# Duplicate rows and update for pool and psuedoreplicates and update tagAlign with single end data
experiment_id = design_df.at[0, 'experiment_id']
replicate_files = design_df.tag_align.unique()
@@ -237,9 +238,9 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
else:
pool_experiment_se = pool_experiment
- # Check controls against cutoff_ratio
- # if so replace with pool_control
- # unless single control was used
+ # Check controls against cutoff_ratio
+ # if so replace with pool_control
+ # unless single control was used
if not single_control:
path_to_pool_control = cwd + '/' + pool_control
if control_df.values.max() > cutoff_ratio:
@@ -267,7 +268,10 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
path_to_control
else:
- path_to_pool_control = pool_control
+ if paired:
+ path_to_pool_control = cwd + '/' + pool_control
+ else:
+ path_to_pool_control = pool_control
design_new_df['control_tag_align'] = path_to_pool_control
# Add in pseudo replicates
--
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