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Diffstat (limited to 'bh20sequploader/qc_fasta.py')
| -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)) |