From 6a389e7f8b44bc19929c67355340693e82a9cd87 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 6 Oct 2017 15:07:05 -0500
Subject: [PATCH] Fix missing variable and naming conventions.
---
workflow/scripts/map_reads.py | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index a15cf45..6ccb5b9 100644
--- a/workflow/scripts/map_reads.py
+++ b/workflow/scripts/map_reads.py
@@ -160,6 +160,8 @@ def align_pe(fastq, sai, reference, fastq_basename):
def main():
args = get_args()
paired = args.paired
+ fastq = args.fastq
+ reference = args.reference
# Create a file handler
handler = logging.FileHandler('map.log')
@@ -170,8 +172,8 @@ def main():
# Run Suffix Array generation
sai = []
- for fastq in args.fastq:
- sai_filename = generate_sa(fastq, args.reference)
+ for fq in fastq:
+ sai_filename = generate_sa(fq, reference)
sai.append(sai_filename)
# Run alignment for either PE or SE
@@ -182,13 +184,13 @@ def main():
strip_extensions(fastq[1], STRIP_EXTENSIONS))
fastq_basename = fastq_r1_basename + fastq_r2_basename
- align_pe(fastq, sai, fastq_basename)
+ align_pe(fastq, sai, reference, fastq_basename)
else:
fastq_basename = os.path.basename(
strip_extensions(fastq[0], STRIP_EXTENSIONS))
- align_se(fastq, sai, fastq_basename)
+ align_se(fastq, sai, reference, fastq_basename)
bam_mapstats_filename = '%s.raw.srt.bam.flagstat.qc' % (fastq_basename)
with open(raw_bam_mapstats_filename, 'w') as fh:
--
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