diff options
| author | Peter Amstutz | 2020-04-29 14:30:28 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-29 14:30:28 -0400 |
| commit | fc86359aef7b26e3bd2ba0eedd291ccdde35e0b1 (patch) | |
| tree | 94124a5d29b3cfa05ebad059014a029cbfbc7773 | |
| parent | 5e04bca4c4628faa5a51374c32f137b9100106d0 (diff) | |
| download | bh20-seq-resource-fc86359aef7b26e3bd2ba0eedd291ccdde35e0b1.tar.gz bh20-seq-resource-fc86359aef7b26e3bd2ba0eedd291ccdde35e0b1.tar.lz bh20-seq-resource-fc86359aef7b26e3bd2ba0eedd291ccdde35e0b1.zip | |
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.py | 2 |
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)) |