From 3d77cb5b70850da88b24da4b1b8deb56826d4e04 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 7 Oct 2017 10:46:54 -0500
Subject: [PATCH] update the naming of the reads.
---
workflow/scripts/map_reads.py | 15 ++++++++++-----
1 file changed, 10 insertions(+), 5 deletions(-)
diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index ebce796..972a816 100644
--- a/workflow/scripts/map_reads.py
+++ b/workflow/scripts/map_reads.py
@@ -112,24 +112,27 @@ def align_se(fastq, sai, reference, fastq_basename):
'''Use BWA to align SE data.'''
sam_filename = "%s.sam" % (fastq_basename)
+ bam_filename = '%s.bam' % (fastq_basename)
steps = [
"bwa samse %s %s %s"
% (reference, fastq[0], sai[0]),
"samtools view -@%d -Su -" % (cpu_count()),
"samtools sort -@%d -o %s"
- % (cpu_count(), fastq_basename)]
+ % (cpu_count(), bam_filename)]
out, err = utils.run_pipe(steps)
if err:
logger.error("samse/samtools error: %s" % (err))
+ return bam_filename
def align_pe(fastq, sai, reference, fastq_basename):
'''Use BWA to align PE data.'''
sam_filename = "%s.sam" % (fastq_basename)
badcigar_filename = "%s.badReads" % (fastq_basename)
+ bam_filename = '%s.bam' % (fastq_basename)
# Remove read pairs with bad CIGAR strings and sort by position
steps = [
@@ -150,12 +153,14 @@ def align_pe(fastq, sai, reference, fastq_basename):
"grep -v -F -f %s" % (badcigar_filename),
"samtools view -@%d -Su -" % (cpu_count()),
"samtools sort -@%d -o %s"
- % (cpu_count(), fastq_basename)]
+ % (cpu_count(), bam_filename)]
out, err = utils.run_pipe(steps)
if err:
logger.error("samtools error: %s" % (err))
+ return bam_filename
+
def main():
args = get_args()
@@ -184,18 +189,18 @@ def main():
strip_extensions(fastq[1], STRIP_EXTENSIONS))
fastq_basename = fastq_r1_basename + fastq_r2_basename
- align_pe(fastq, sai, reference, fastq_basename)
+ bam_filename = align_pe(fastq, sai, reference, fastq_basename)
else:
fastq_basename = os.path.basename(
strip_extensions(fastq[0], STRIP_EXTENSIONS))
- align_se(fastq, sai, reference, fastq_basename)
+ bam_filename = align_se(fastq, sai, reference, fastq_basename)
bam_mapstats_filename = '%s.raw.srt.bam.flagstat.qc' % (fastq_basename)
with open(bam_mapstats_filename, 'w') as fh:
subprocess.check_call(
- shlex.split("samtools flagstat %s" % (bam_mapstats_filename)),
+ shlex.split("samtools flagstat %s" % (bam_filename)),
stdout=fh)
# Remove sai files
--
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