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| author | Peter Amstutz | 2020-07-03 21:15:48 +0000 |
|---|---|---|
| committer | Peter Amstutz | 2020-07-03 21:15:48 +0000 |
| commit | 38340e0cedb465cd592ac40b11c9d22c75973fed (patch) | |
| tree | 92e9834c68edcb93a6597d091b337318675af33d /bh20sequploader/qc_fasta.py | |
| parent | 04df498f5cd85015afce79e1e87a3979e596dcc6 (diff) | |
| download | bh20-seq-resource-38340e0cedb465cd592ac40b11c9d22c75973fed.tar.gz bh20-seq-resource-38340e0cedb465cd592ac40b11c9d22c75973fed.tar.lz bh20-seq-resource-38340e0cedb465cd592ac40b11c9d22c75973fed.zip | |
Add --skip-qc for faster batch import
Diffstat (limited to 'bh20sequploader/qc_fasta.py')
| -rw-r--r-- | bh20sequploader/qc_fasta.py | 6 |
1 files changed, 3 insertions, 3 deletions
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py index 944b52c..8c6ebd3 100644 --- a/bh20sequploader/qc_fasta.py +++ b/bh20sequploader/qc_fasta.py @@ -54,6 +54,9 @@ def qc_fasta(arg_sequence, check_with_clustalw=True): sequence.seek(0) sequence.detach() + if not check_with_clustalw: + return ("sequence.fasta"+gz, seqlabel) + with tempfile.NamedTemporaryFile() as tmp1: refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta") tmp1.write(refstring) @@ -64,9 +67,6 @@ def qc_fasta(arg_sequence, check_with_clustalw=True): refbp = 0 similarity = 0 try: - if not check_with_clustalw: - raise Exception("skipping QC") - cmd = ["clustalw", "-infile="+tmp1.name, "-quicktree", "-iteration=none", "-type=DNA"] print("QC checking similarity to reference") |