From bbeb4524e8e66710e1dac48e443362382af98409 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 15 Nov 2017 13:21:12 -0600
Subject: [PATCH] Changed to bedSort.
---
workflow/scripts/call_peaks_macs.py | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py
index e670496..37ac6ac 100644
--- a/workflow/scripts/call_peaks_macs.py
+++ b/workflow/scripts/call_peaks_macs.py
@@ -175,8 +175,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
# Sort file
out, err = utils.run_pipe([
- 'sort -k1,1 -k2,2n %s' % (fc_bedgraph_fn)],
- fc_bedgraph_sorted_fn)
+ 'bedSort %s %s' % (fc_bedgraph_fn, fc_bedgraph_sorted_fn)])
# Convert bedgraph to bigwig
command = 'bedGraphToBigWig ' + \
@@ -223,8 +222,7 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
# Sort file
out, err = utils.run_pipe([
- 'sort -k1,1 -k2,2n %s' % (fc_bedgraph_fn)],
- pvalue_bedgraph_sorted_fn)
+ 'bedSort %s %s' % (fc_bedgraph_fn, pvalue_bedgraph_sorted_fn)])
# Convert bedgraph to bigwig
command = 'bedGraphToBigWig ' + \
--
GitLab