From 4aa91a5c825a2034924d97430416fbc97fa1ba9e Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sun, 13 Jan 2019 16:09:41 -0600
Subject: [PATCH] Update file name output.
---
workflow/scripts/motif_search.py | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/workflow/scripts/motif_search.py b/workflow/scripts/motif_search.py
index a7f6d1a..02e316f 100644
--- a/workflow/scripts/motif_search.py
+++ b/workflow/scripts/motif_search.py
@@ -84,13 +84,18 @@ def motif_search(filename, genome, experiment, peak):
file_basename = os.path.basename(
utils.strip_extensions(filename, STRIP_EXTENSIONS))
- sorted_fn = '%s.%d.narrowPeak' % (file_basename, peak)
+
out_fa = '%s.fa' % (experiment)
out_motif = '%s_memechip' % (experiment)
# Sort Bed file and limit number of peaks
if peak == -1:
peak = utils.count_lines(filename)
+ peak_no = 'all'
+ else:
+ peak_no = peak
+
+ sorted_fn = '%s.%s.narrowPeak' % (file_basename, peak)
out, err = utils.run_pipe([
'sort -k %dgr,%dgr %s' % (5, 5, filename),
--
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