aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--bh20sequploader/main.py9
-rw-r--r--bh20sequploader/qc_fasta.py7
2 files changed, 10 insertions, 6 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 89c30e8..dc63bfc 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -22,10 +22,10 @@ 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):
try:
log.debug("Checking metadata")
- if not qc_metadata(metadata.name):
+ if do_qc and not qc_metadata(metadata.name):
log.warning("Failed metadata qc")
exit(1)
except ValueError as e:
@@ -37,7 +37,7 @@ def qa_stuff(metadata, sequence_p1, sequence_p2):
target = []
try:
log.debug("Checking FASTA/FASTQ QC")
- target.append(qc_fasta(sequence_p1))
+ 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])
@@ -64,11 +64,12 @@ def main():
parser.add_argument('sequence_p1', type=argparse.FileType('rb'), 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")
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:
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index 1587def..944b52c 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -25,7 +25,7 @@ def read_fasta(sequence):
raise ValueError("FASTA file contains multiple entries")
return label, bases
-def qc_fasta(arg_sequence):
+def qc_fasta(arg_sequence, check_with_clustalw=True):
log.debug("Starting qc_fasta")
schema_resource = pkg_resources.resource_stream(__name__, "validation/formats")
with tempfile.NamedTemporaryFile() as tmp:
@@ -64,6 +64,9 @@ def qc_fasta(arg_sequence):
refbp = 0
similarity = 0
try:
+ if not check_with_clustalw:
+ raise Exception("skipping QC")
+
cmd = ["clustalw", "-infile="+tmp1.name,
"-quicktree", "-iteration=none", "-type=DNA"]
print("QC checking similarity to reference")
@@ -81,7 +84,7 @@ def qc_fasta(arg_sequence):
print(g2.group(0))
print(g3.group(0))
except Exception as e:
- logging.warn("Error trying to QC against reference sequence using 'clustalw': %s", e)
+ logging.warn("QC against reference sequence using 'clustalw': %s", e)
if refbp and (subbp/refbp) < .7:
raise ValueError("QC fail: submit sequence length is shorter than 70% reference")