diff options
Diffstat (limited to 'bh20sequploader/main.py')
| -rw-r--r-- | bh20sequploader/main.py | 22 |
1 files changed, 17 insertions, 5 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 17ad492..56cbe22 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -6,6 +6,7 @@ import json import urllib.request import socket import getpass +from .qc_metadata import qc_metadata ARVADOS_API_HOST='lugli.arvadosapi.com' ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' @@ -19,18 +20,26 @@ def main(): api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) + 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: + if args.sequence.name.endswith("fasta") or args.sequence.name.endswith("fa"): + target = "sequence.fasta" + elif args.sequence.name.endswith("fastq") or args.sequence.name.endswith("fq"): + target = "reads.fastq" + + 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) - 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: @@ -49,4 +58,7 @@ def main(): (properties['upload_user'], properties['upload_ip']), properties=properties, ensure_unique_name=True) -main() + print("Done") + +if __name__ == "__main__": + main() |