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authorPeter Amstutz2020-11-11 17:38:16 -0500
committerPeter Amstutz2020-11-11 17:38:47 -0500
commit2cb5faa2b088cf36c8c41633db137fc020a34529 (patch)
tree6a9f39513e020517f2bac609aaf2e15128411a70 /bh20sequploader
parentc5c730cdeb9f2e9a02e30c2215dfe2b6ae787b07 (diff)
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Support uploading new metadata only
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'bh20sequploader')
-rw-r--r--bh20sequploader/main.py48
1 files changed, 26 insertions, 22 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index ea0fa70..e2f089f 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -52,23 +52,23 @@ sequence for enough overlap with the reference genome
failed = True # continue with the FASTA checker
target = []
- try:
- log.debug("FASTA/FASTQ QC" if do_qc else "Limited FASTA/FASTQ QC")
- target.append(qc_fasta(sequence_p1, check_with_mimimap2=do_qc))
- if sequence_p2:
- if target[0][2] == 'text/fasta':
- raise ValueError("It is possible to upload just one FASTA file at a time")
- target.append(qc_fasta(sequence_p2))
-
- target[0] = ("reads_1."+target[0][0][6:], target[0][1], target[0][2])
- target[1] = ("reads_2."+target[1][0][6:], target[1][1], target[1][2])
-
- if do_qc and target[0][2] == 'text/fasta' and sample_id != target[0][1]:
- raise ValueError(f"The sample_id field in the metadata ({sample_id}) must be the same as the FASTA header ({target[0][1]})")
-
- except Exception as e:
- log.exception("Failed sequence QC")
- failed = True
+ if sequence_p1:
+ try:
+ log.debug("FASTA/FASTQ QC" if do_qc else "Limited FASTA/FASTQ QC")
+ target.append(qc_fasta(sequence_p1, check_with_mimimap2=do_qc))
+ if sequence_p2:
+ if target[0][2] == 'text/fasta':
+ raise ValueError("It is possible to upload just one FASTA file at a time")
+ target.append(qc_fasta(sequence_p2))
+
+ target[0] = ("reads_1."+target[0][0][6:], target[0][1], target[0][2])
+ target[1] = ("reads_2."+target[1][0][6:], target[1][1], target[1][2])
+
+ if do_qc and target[0][2] == 'text/fasta' and sample_id != target[0][1]:
+ raise ValueError(f"The sample_id field in the metadata ({sample_id}) must be the same as the FASTA header ({target[0][1]})")
+ except Exception as e:
+ log.exception("Failed sequence QC")
+ failed = True
if failed:
log.debug("Bailing out!")
@@ -87,7 +87,7 @@ def upload_sequence(col, target, sequence):
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_p1', type=argparse.FileType('rb'), default=None, nargs='?', help='sequence FASTA/FASTQ')
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")
@@ -102,7 +102,10 @@ def main():
# ---- First the QC
target = qc_stuff(args.metadata, args.sequence_p1, args.sequence_p2, not args.skip_qc)
- seqlabel = target[0][1]
+ if target:
+ seqlabel = target[0][1]
+ else:
+ seqlabel = ""
if args.validate:
log.info("Valid")
@@ -111,9 +114,10 @@ def main():
col = arvados.collection.Collection(api_client=api)
# ---- Upload the sequence to Arvados
- upload_sequence(col, target[0], args.sequence_p1)
- if args.sequence_p2:
- upload_sequence(col, target[1], args.sequence_p2)
+ if args.sequence_p1:
+ upload_sequence(col, target[0], args.sequence_p1)
+ if args.sequence_p2:
+ upload_sequence(col, target[1], args.sequence_p2)
# ---- Make sure the metadata YAML is valid
log.info("Reading metadata")