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-rw-r--r--bh20sequploader/main.py16
1 files changed, 12 insertions, 4 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 8b8fefe..bf74ea5 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -6,7 +6,7 @@ import json
import urllib.request
import socket
import getpass
-from .qc_metadata import qc_metadata
+import qc_metadata
ARVADOS_API_HOST='lugli.arvadosapi.com'
ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
@@ -20,12 +20,18 @@ def main():
api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
- qc_metadata(args.metadata.name)
+ 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:
@@ -52,5 +58,7 @@ def main():
(properties['upload_user'], properties['upload_ip']),
properties=properties, ensure_unique_name=True)
+ print("Done")
+
if __name__ == "__main__":
main()