From fed7c7837c186980999d3b1b6f5d9c0db6998167 Mon Sep 17 00:00:00 2001
From: Holly Ruess <s185797@biohpcwsc012.biohpc.swmed.edu>
Date: Thu, 26 Dec 2019 15:24:30 -0600
Subject: [PATCH] fix pool and pseudo
---
workflow/scripts/pool_and_psuedoreplicate.py | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 9a01e6b..7b6fbc9 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -133,7 +133,7 @@ def self_psuedoreplication(tag_file, prefix, paired):
# Convert read pairs to reads into standard tagAlign file
for i, index in enumerate([0, 1]):
- string_index = '0' + str(index)
+ string_index = '.0' + str(index)
steps = ['cat %s' % (splits_prefix + string_index)]
if paired:
steps.extend([r"""awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}'"""])
@@ -272,7 +272,9 @@ def main():
# Update tagAlign with single end data
if paired:
design_new_df['tag_align'] = design_new_df['se_tag_align']
- design_new_df.drop(labels='se_tag_align', axis=1, inplace=True)
+
+# design_new_df.drop(labels='se_tag_align', axis=1, inplace=True)
+ design_new_df.drop(labels='tag_align', axis=1, inplace=True)
# Check controls against cutoff_ratio
# if so replace with pool_control
--
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