From fc86359aef7b26e3bd2ba0eedd291ccdde35e0b1 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 29 Apr 2020 14:30:28 -0400 Subject: Use subprocess invocation is backwards compatible with Python 3.5 Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- bh20sequploader/qc_fasta.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'bh20sequploader') diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py index 2600cfa..16cf2c9 100644 --- a/bh20sequploader/qc_fasta.py +++ b/bh20sequploader/qc_fasta.py @@ -46,7 +46,7 @@ def qc_fasta(sequence): "-quicktree", "-iteration=none", "-type=DNA"] print("QC checking similarity to reference") print(" ".join(cmd)) - result = subprocess.run(cmd, capture_output=True) + result = subprocess.run(cmd, stdout=subprocess.PIPE) res = result.stdout.decode("utf-8") g1 = re.search(r"^Sequence 1: [^ ]+ +(\d+) bp$", res, flags=re.MULTILINE) refbp = float(g1.group(1)) -- cgit v1.2.3