From 0a9794c2dfd22f4f086eec53db232410eb287bbd Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sun, 29 Oct 2017 20:06:04 -0500
Subject: [PATCH] Fix string of index.
---
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 7b5d636..f879681 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -124,13 +124,14 @@ def self_psuedoreplication(tag_file, prefix, paired):
# Convert read pairs to reads into standard tagAlign file
- for i, string(index) in enumerate([0, 1]):
- steps = ['cat %s' % (splits_prefix + index)]
+ for i, index in enumerate([0, 1]):
+ string_index = 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}'"""])
steps.extend(['gzip -cn'])
out, err = utils.run_pipe(steps, outfile=pseudoreplicate_dict[i])
- os.remove(splits_prefix + index)
+ os.remove(splits_prefix + string_index)
return pseudoreplicate_dict
--
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