From efc98ccc2d276330d53ccfe680ea67a4ca4707dd Mon Sep 17 00:00:00 2001
From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu>
Date: Thu, 18 Jul 2019 08:58:12 -0500
Subject: [PATCH] redo replicate
---
workflow/scripts/pool_and_psuedoreplicate.py | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index c8042f5..54ca187 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -229,14 +229,14 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
design_new_df.at[3, 'tag_align'] = design_new_df.at[0, 'tag_align']
# Make 2 self psuedoreplicates
- self_pseudoreplicates_dict = {}
+ pool_pseudoreplicates_dict = {}
for rep, tag_file in zip(design_df['replicate'], design_df['tag_align']):
replicate_prefix = experiment_id + '_' + str(rep)
- self_pseudoreplicates_dict = \
+ pool_pseudoreplicates_dict = \
self_psuedoreplication(tag_file, replicate_prefix, paired)
# Update design to include new self pseudo replicates
- for rep, pseudorep_file in self_pseudoreplicates_dict.items():
+ for rep, pseudorep_file in pool_pseudoreplicates_dict.items():
path_to_file = cwd + '/' + pseudorep_file
replicate = rep + 1
design_new_df.loc[replicate, 'tag_align'] = path_to_file
@@ -262,6 +262,7 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
replicate_prefix = experiment_id + '_' + str(rep)
pr_dict = self_psuedoreplication(tag_file, replicate_prefix, paired)
pseudoreplicates_dict[rep] = pr_dict
+
# Merge self psuedoreplication for each true replicate
pseudoreplicates_df = pd.DataFrame.from_dict(pseudoreplicates_dict)
pool_pseudoreplicates_dict = {}
--
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