From bb44fc95e1ae7e6598a1d3c8c5589a515b139d5f Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 14 Nov 2017 19:49:14 -0600
Subject: [PATCH] Fix parsing of fraglength.
---
workflow/scripts/call_peaks_macs.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/workflow/scripts/call_peaks_macs.py b/workflow/scripts/call_peaks_macs.py
index 1031bc8..c89c12e 100644
--- a/workflow/scripts/call_peaks_macs.py
+++ b/workflow/scripts/call_peaks_macs.py
@@ -98,7 +98,8 @@ def call_peaks_macs(experiment, xcor, control, prefix, genome_size, chrom_sizes)
# cross-correlation scores file
with open(xcor, 'r') as xcor_fh:
firstline = xcor_fh.readline()
- fragment_length = firstline.split()[2] # third column
+ frag_lengths = firstline.split()[2] # third column
+ fragment_length = frag_lengths.split(',')[0] # grab first value
logger.info("Fraglen %s" % (fragment_length))
--
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