diff options
Diffstat (limited to 'bh20sequploader/main.py')
| -rw-r--r-- | bh20sequploader/main.py | 29 |
1 files changed, 16 insertions, 13 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index c442af0..fd0278d 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -22,30 +22,32 @@ ARVADOS_API_HOST='lugli.arvadosapi.com' ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa' -def qa_stuff(metadata, sequence_p1, sequence_p2): +def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): + failed = False try: - log.debug("Checking metadata") - if not qc_metadata(metadata.name): + 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) - except ValueError as e: + failed = True + except Exception as e: log.debug(e) - log.debug("Failed metadata qc") print(e) - exit(1) + failed = True target = [] try: - log.debug("Checking FASTA/FASTQ QC") - target.append(qc_fasta(sequence_p1)) + 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)) target[0] = ("reads_1."+target[0][0][6:], target[0][1]) target[1] = ("reads_2."+target[1][0][6:], target[0][1]) - except ValueError as e: + except Exception as e: log.debug(e) - log.debug("Failed FASTA qc") print(e) + failed = True + + if failed: exit(1) return target @@ -62,13 +64,14 @@ def main(): parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis') parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json') parser.add_argument('sequence_p1', type=argparse.FileType('rb'), help='sequence FASTA/FASTQ') - parser.add_argument('sequence_p2', type=argparse.FileType('rb'), default=None, help='sequence FASTQ pair') + parser.add_argument('sequence_p2', type=argparse.FileType('rb'), default=None, nargs='?', help='sequence FASTQ pair') parser.add_argument("--validate", action="store_true", help="Dry run, validate only") + parser.add_argument("--skip-qc", action="store_true", help="Skip local qc check") args = parser.parse_args() api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) - target = qa_stuff(args.metadata, args.sequence_p1, args.sequence_p2) + target = qc_stuff(args.metadata, args.sequence_p1, args.sequence_p2, not args.skip_qc) seqlabel = target[0][1] if args.validate: |