From f54c2d8833117f3472523521fe5ce50f9a5fd2ac Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 26 Jun 2018 17:14:51 -0500
Subject: [PATCH] Update convert reads.
---
workflow/scripts/convert_reads.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/workflow/scripts/convert_reads.py b/workflow/scripts/convert_reads.py
index c3268da..eb805a8 100644
--- a/workflow/scripts/convert_reads.py
+++ b/workflow/scripts/convert_reads.py
@@ -84,9 +84,9 @@ def convert_mapped(bam, tag_filename, chrm):
r"""awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}'"""]
if chrm:
- steps.extend["grep -v 'chrM'"]
+ steps.extend(["grep -v 'chrM'"])
- steps.extend["gzip -nc"]
+ steps.extend(["gzip -nc"])
out, err = utils.run_pipe(steps, outfile=tag_filename)
@@ -107,13 +107,13 @@ def convert_mapped_pe(bam, bam_basename, tag_filename, chrm):
steps = ["bamToBed -bedpe -mate1 -i %s" % (nmsrt_bam_filename)]
- steps.extend["gzip -nc"]
+ steps.extend(["gzip -nc"])
out, err = utils.run_pipe(steps, outfile=bedpe_filename)
os.remove(nmsrt_bam_filename)
if chrm:
- steps.extend["grep -v 'chrM'"]
+ steps.extend(["grep -v 'chrM'"])
# Convert read pairs to reads into standard tagAlign file
tag_steps = ["zcat -f %s" % (bedpe_filename)]
--
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