From ec7373607d81a06aa9ac63479b3f3bf7657aaa3b Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 17 Dec 2018 10:54:20 -0600
Subject: [PATCH] Defaulted to zcat instead of unzip file.
---
workflow/scripts/xcor.py | 14 +++++++-------
1 file changed, 7 insertions(+), 7 deletions(-)
diff --git a/workflow/scripts/xcor.py b/workflow/scripts/xcor.py
index 5283859..f799137 100644
--- a/workflow/scripts/xcor.py
+++ b/workflow/scripts/xcor.py
@@ -61,20 +61,20 @@ def xcor(tag, paired):
'''Use spp to calculate cross-correlation stats.'''
tag_basename = os.path.basename(utils.strip_extensions(tag, ['.gz']))
-
uncompressed_tag_filename = tag_basename
- out, err = utils.run_pipe([
- 'gzip -dc %s > ' % (tag)], outfile=uncompressed_tag_filename)
+
# Subsample tagAlign file
NREADS = 15000000
-
subsampled_tag_filename = \
tag_basename + ".%d.tagAlign.gz" % (NREADS/1000000)
+
+
steps = [
- 'grep -v "chrM" %s' % (uncompressed_tag_filename),
- 'shuf -n %d --random-source=%s' % (NREADS, uncompressed_tag_filename)
- ]
+ 'zcat %s' % (tag),
+ 'grep -v "chrM"',
+ 'shuf -n %d --random-source=%s' % (NREADS, tag)]
+
if paired:
steps.extend([r"""awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}'"""])
--
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