From e6c55f505e5c4f18cbb124801bf12495a0be5f19 Mon Sep 17 00:00:00 2001
From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu>
Date: Thu, 25 Jul 2019 15:20:39 -0500
Subject: [PATCH] Re order pool and pseudoreplicates
---
workflow/scripts/pool_and_psuedoreplicate.py | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 9ad35fa..2c35772 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -210,6 +210,7 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
experiment_id = design_df.at[0, 'experiment_id']
replicate = design_df.at[0, 'replicate']
design_new_df = design_df.loc[np.repeat(design_df.index, 4)].reset_index()
+ pool_experiment = design_df.tag_align.unique()
# Update tagAlign with single end data
if paired:
@@ -250,12 +251,6 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
experiment_id = design_df.at[0, 'experiment_id']
pool_experiment = pool(replicate_files, experiment_id + "_pooled", paired)
- # If paired change to single End
- if paired:
- pool_experiment_se = bedpe_to_tagalign(pool_experiment, experiment_id + "_pooled")
- else:
- pool_experiment_se = pool_experiment
-
# Make self psuedoreplicates equivalent to number of replicates
pseudoreplicates_dict = {}
for rep, tag_file in zip(design_df['replicate'], design_df['tag_align']):
@@ -281,6 +276,11 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
# if so replace with pool_control
# unless single control was used
+ # If paired change to single End
+ if paired:
+ pool_experiment_se = bedpe_to_tagalign(pool_experiment, experiment_id + "_pooled")
+ else:
+ pool_experiment_se = pool_experiment
if not single_control:
path_to_pool_control = cwd + '/' + pool_control
--
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