From 07e414587ad8f72da9c895da1389d4f9a044bcec Mon Sep 17 00:00:00 2001
From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu>
Date: Thu, 18 Jul 2019 09:19:29 -0500
Subject: [PATCH] fix indentation in pool and pseudoreplicate
---
workflow/scripts/pool_and_psuedoreplicate.py | 36 ++++++++++----------
1 file changed, 18 insertions(+), 18 deletions(-)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 54ca187..b428b0b 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
- pool_pseudoreplicates_dict = {}
+ self_pseudoreplicates_dict = {}
for rep, tag_file in zip(design_df['replicate'], design_df['tag_align']):
replicate_prefix = experiment_id + '_' + str(rep)
- pool_pseudoreplicates_dict = \
+ self_pseudoreplicates_dict = \
self_psuedoreplication(tag_file, replicate_prefix, paired)
# Update design to include new self pseudo replicates
- for rep, pseudorep_file in pool_pseudoreplicates_dict.items():
+ for rep, pseudorep_file in self_pseudoreplicates_dict.items():
path_to_file = cwd + '/' + pseudorep_file
replicate = rep + 1
design_new_df.loc[replicate, 'tag_align'] = path_to_file
@@ -312,25 +312,25 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
path_to_pool_control = cwd + '/' + pool_control
design_new_df['control_tag_align'] = path_to_pool_control
- # Add in pseudo replicates
- tmp_metadata = design_new_df.loc[0].copy()
- tmp_metadata['control_tag_align'] = path_to_pool_control
- for rep, pseudorep_file in pool_pseudoreplicates_dict.items():
- tmp_metadata['sample_id'] = experiment_id + '_pr' + str(rep)
- tmp_metadata['replicate'] = str(rep) + '_pr'
+ # Add in pseudo replicates
+ tmp_metadata = design_new_df.loc[0].copy()
+ tmp_metadata['control_tag_align'] = path_to_pool_control
+ for rep, pseudorep_file in pool_pseudoreplicates_dict.items():
+ tmp_metadata['sample_id'] = experiment_id + '_pr' + str(rep)
+ tmp_metadata['replicate'] = str(rep) + '_pr'
+ tmp_metadata['xcor'] = 'Calculate'
+ path_to_file = cwd + '/' + pseudorep_file
+ tmp_metadata['tag_align'] = path_to_file
+ design_new_df = design_new_df.append(tmp_metadata)
+
+ # Add in pool experiment
+ tmp_metadata['sample_id'] = experiment_id + '_pooled'
+ tmp_metadata['replicate'] = 'pooled'
tmp_metadata['xcor'] = 'Calculate'
- path_to_file = cwd + '/' + pseudorep_file
+ path_to_file = cwd + '/' + pool_experiment_se
tmp_metadata['tag_align'] = path_to_file
design_new_df = design_new_df.append(tmp_metadata)
- # Add in pool experiment
- tmp_metadata['sample_id'] = experiment_id + '_pooled'
- tmp_metadata['replicate'] = 'pooled'
- tmp_metadata['xcor'] = 'Calculate'
- path_to_file = cwd + '/' + pool_experiment_se
- tmp_metadata['tag_align'] = path_to_file
- design_new_df = design_new_df.append(tmp_metadata)
-
return design_new_df
--
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