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authorPeter Amstutz2020-04-29 14:30:28 -0400
committerPeter Amstutz2020-04-29 14:30:28 -0400
commitfc86359aef7b26e3bd2ba0eedd291ccdde35e0b1 (patch)
tree94124a5d29b3cfa05ebad059014a029cbfbc7773
parent5e04bca4c4628faa5a51374c32f137b9100106d0 (diff)
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Use subprocess invocation is backwards compatible with Python 3.5
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
-rw-r--r--bh20sequploader/qc_fasta.py2
1 files changed, 1 insertions, 1 deletions
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))