From 79526d57a116e4bbb331b94f13cf59fc18866da7 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 24 Oct 2017 13:11:08 -0500
Subject: [PATCH] Fix output.
---
workflow/scripts/xcor.py | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/workflow/scripts/xcor.py b/workflow/scripts/xcor.py
index 484e84a..88750b6 100644
--- a/workflow/scripts/xcor.py
+++ b/workflow/scripts/xcor.py
@@ -5,7 +5,6 @@
import os
import argparse
import shutil
-import shlex
import logging
from multiprocessing import cpu_count
import utils
@@ -60,17 +59,17 @@ def check_tools():
def xcor(tag, paired):
'''Use spp to calculate cross-correlation stats.'''
- tag_basename = tag.rstrip('.gz')
+ tag_basename = os.path.basename(utils.strip_extensions(tag, ['.gz']))
uncompressed_tag_filename = tag_basename
- out, err = utils.run_pipe(['gzip -d %s' % (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)
+ 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)
--
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