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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 | |
| 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')
| -rw-r--r-- | bh20sequploader/main.py | 4 | ||||
| -rw-r--r-- | bh20sequploader/qc_fasta.py | 6 |
2 files changed, 5 insertions, 5 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index dc63bfc..cdc4c3f 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -24,7 +24,7 @@ UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa' def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): try: - log.debug("Checking metadata") + log.debug("Checking metadata" if do_qc else "Skipping metadata check") if do_qc and not qc_metadata(metadata.name): log.warning("Failed metadata qc") exit(1) @@ -36,7 +36,7 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): target = [] try: - log.debug("Checking FASTA/FASTQ QC") + log.debug("FASTA/FASTQ QC" if do_qc else "Limited FASTA/FASTQ QC") target.append(qc_fasta(sequence_p1, check_with_clustalw=do_qc)) if sequence_p2: target.append(qc_fasta(sequence_p2)) 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") |