From b8588c1a69e3336161964cae5934514946feb539 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 10 Oct 2017 15:11:22 -0500
Subject: [PATCH] Update files used.
---
workflow/scripts/map_qc.py | 13 +++++++------
1 file changed, 7 insertions(+), 6 deletions(-)
diff --git a/workflow/scripts/map_qc.py b/workflow/scripts/map_qc.py
index fe47bc3..f44b6e4 100644
--- a/workflow/scripts/map_qc.py
+++ b/workflow/scripts/map_qc.py
@@ -166,7 +166,6 @@ def dedup_mapped(bam, bam_basename, paired):
shlex.split(sambamba_markdup_command),
stderr=fh)
- os.remove(tmp_dup_mark_filename + '.bai')
# Remove duplicates
final_bam_prefix = bam_basename + ".filt.nodup"
@@ -174,10 +173,10 @@ def dedup_mapped(bam, bam_basename, paired):
if paired: # paired-end data
samtools_dedupe_command = \
- "samtools view -F 1804 -f 2 -b %s" % (bam)
+ "samtools view -F 1804 -f 2 -b %s" % (tmp_dup_mark_filename)
else:
samtools_dedupe_command = \
- "samtools view -F 1804 -b %s" % (bam)
+ "samtools view -F 1804 -b %s" % (tmp_dup_mark_filename)
with open(final_bam_filename, 'w') as fh:
logger.info(samtools_dedupe_command)
@@ -200,7 +199,7 @@ def dedup_mapped(bam, bam_basename, paired):
subprocess.check_call(shlex.split(flagstat_command), stdout=fh)
os.remove(bam)
- return final_bam_filename
+ return tmp_dup_mark_filename
def compute_complexity(bam, paired, bam_basename):
@@ -253,6 +252,8 @@ def compute_complexity(bam, paired, bam_basename):
pbc_file = pd.read_csv(tmp_pbc_file_qc_filename, sep='\t', header=None,
names=pbc_headers)
pbc_file.to_csv(pbc_file_qc_filename, header=True, sep='\t', index=False)
+ os.remove(bam)
+ os.remove(bam + '.bai')
os.remove(tmp_pbc_file_qc_filename)
@@ -278,10 +279,10 @@ def main():
filter_bam_filename = filter_mapped_se(bam, bam_basename)
# Remove duplicates
- dedup_bam_filename = dedup_mapped(filter_bam_filename, bam_basename, paired)
+ markdup_bam_filename = dedup_mapped(filter_bam_filename, bam_basename, paired)
# Compute library complexity
- compute_complexity(dedup_bam_filename, paired, bam_basename)
+ compute_complexity(markdup_bam_filename, paired, bam_basename)
if __name__ == '__main__':
--
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