From 38d866fe71749b17f2636c41565e56c83117f385 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 14 Nov 2017 19:35:04 -0600
Subject: [PATCH] Fix xcor to be calucated and updated the pseudoreplicate
names.
---
workflow/scripts/pool_and_psuedoreplicate.py | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 6dbe7c9..318c037 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -190,17 +190,20 @@ def main():
replicate = design_df.at[0, 'replicate']
design_new_df = design_df.loc[np.repeat(design_df.index, 4)].reset_index()
design_new_df['replicate'] = design_new_df['replicate'].astype(str)
- design_new_df.at[1, 'sample_id'] = experiment_id + '_pr'
+ design_new_df.at[1, 'sample_id'] = experiment_id + '_pr1'
design_new_df.at[1, 'replicate'] = '1_pr'
- design_new_df.at[2, 'sample_id'] = experiment_id + '_pr'
+ design_new_df.at[1,'xcor'] = 'Calculate'
+ design_new_df.at[2, 'sample_id'] = experiment_id + '_pr2'
design_new_df.at[2, 'replicate'] = '2_pr'
- design_new_df.at[3, 'sample_id'] = experiment_id + '_pr'
+ design_new_df.at[2,'xcor'] = 'Calculate'
+ design_new_df.at[3, 'sample_id'] = experiment_id + 'pooled'
design_new_df.at[3, 'replicate'] = 'pooled'
+ design_new_df.at[3,'xcor'] = 'Calculate'
# Make 2 self psuedoreplicates
self_pseudoreplicates_dict = {}
for rep, tag_file in zip(design_df['replicate'], design_df['tag_align']):
- replicate_prefix = experiment_id + '_' + rep
+ replicate_prefix = experiment_id + '_' + str(rep)
self_pseudoreplicates_dict = \
self_psuedoreplication(tag_file, replicate_prefix, paired)
--
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