diff options
Diffstat (limited to 'bh20sequploader/main.py')
| -rw-r--r-- | bh20sequploader/main.py | 26 |
1 files changed, 20 insertions, 6 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 17ad492..4a225f6 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -3,9 +3,13 @@ import time import arvados import arvados.collection import json +import magic +from pathlib import Path import urllib.request import socket import getpass +from .qc_metadata import qc_metadata +from .qc_fasta import qc_fasta ARVADOS_API_HOST='lugli.arvadosapi.com' ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' @@ -13,29 +17,36 @@ UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa' def main(): parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis') - parser.add_argument('sequence', type=argparse.FileType('r'), help='sequence FASTA') + parser.add_argument('sequence', type=argparse.FileType('r'), help='sequence FASTA/FASTQ') parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json') args = parser.parse_args() api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) + target = qc_fasta(args.sequence) + + if not qc_metadata(args.metadata.name): + print("Failed metadata qc") + exit(1) + col = arvados.collection.Collection(api_client=api) - print("Reading FASTA") - with col.open("sequence.fasta", "w") as f: + with col.open(target, "w") as f: r = args.sequence.read(65536) print(r[0:20]) while r: f.write(r) r = args.sequence.read(65536) + args.sequence.close() - print("Reading JSONLD") - with col.open("metadata.jsonld", "w") as f: + print("Reading metadata") + with col.open("metadata.yaml", "w") as f: r = args.metadata.read(65536) print(r[0:20]) while r: f.write(r) r = args.metadata.read(65536) + args.metadata.close() external_ip = urllib.request.urlopen('https://ident.me').read().decode('utf8') @@ -49,4 +60,7 @@ def main(): (properties['upload_user'], properties['upload_ip']), properties=properties, ensure_unique_name=True) -main() + print("Done") + +if __name__ == "__main__": + main() |