From 888267b41c2a5db4d670597310f4f59882648624 Mon Sep 17 00:00:00 2001 From: AroneyS Date: Thu, 2 Nov 2023 10:17:10 +1000 Subject: [PATCH] fix non-gzip open gzip.open defaults to binary mode --- aviary/modules/quality_control/scripts/qc_short_reads.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/aviary/modules/quality_control/scripts/qc_short_reads.py b/aviary/modules/quality_control/scripts/qc_short_reads.py index 2f0fd3fb..b6ff96ce 100755 --- a/aviary/modules/quality_control/scripts/qc_short_reads.py +++ b/aviary/modules/quality_control/scripts/qc_short_reads.py @@ -28,8 +28,8 @@ def setup_interleave(reads_1: str, reads_2: str, output_fastq: str, logf): with gzip.open(reads_2) as f2: interleave(f1, f2, output_fastq) else: - with open(reads_1) as f1: - with open(reads_2) as f2: + with open(reads_1, 'rb') as f1: + with open(reads_2, 'rb') as f2: interleave(f1, f2, output_fastq) def cat_reads(read_path: str, output_path: str, threads: int, log: str):