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authorlltommy2020-07-07 23:58:50 +0200
committerlltommy2020-07-07 23:58:50 +0200
commitc8ffc952a99dc0a2d1266cdc0636711ec63e8bfb (patch)
treed8672cca90c8469f07c20cb80fdbf0439913623a /bh20sequploader/main.py
parent027d7bd6dd89c62a1e81bbda0e6ef7f27cbb3920 (diff)
parentb994b59963248a301e1248f792f21d9ab2ea8a3f (diff)
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Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
Diffstat (limited to 'bh20sequploader/main.py')
-rw-r--r--bh20sequploader/main.py29
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: