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authorPeter Amstutz2020-06-22 16:32:54 +0000
committerPeter Amstutz2020-06-22 16:32:54 +0000
commit4001368ab29c988e94dddd29767c4b64a5bd2a5b (patch)
tree5642bf6a5cd02bc76b0aa98ae086b010f5131cf0
parent7daa9ff2cdba742a811db00c924ccde25fa2c9b6 (diff)
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Better invalid sequence QC handling
-rw-r--r--bh20seqanalyzer/main.py36
-rw-r--r--bh20sequploader/qc_fasta.py11
2 files changed, 27 insertions, 20 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 794ce27..9164190 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -39,22 +39,25 @@ def validate_upload(api, collection, validated_project,
logging.warn("Failed metadata qc")
if valid:
- tgt = None
- paired = {"reads_1.fastq": "reads.fastq", "reads_1.fastq.gz": "reads.fastq.gz"}
- for n in ("sequence.fasta", "reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"):
- if n not in col:
- continue
- with col.open(n, 'rb') as qf:
- tgt = qc_fasta(qf)[0]
- if tgt != n and tgt != paired.get(n):
- logging.info("Expected %s but magic says it should be %s", n, tgt)
- valid = False
- elif tgt in ("reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"):
- start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid, n)
- return False
- if tgt is None:
+ try:
+ tgt = None
+ paired = {"reads_1.fastq": "reads.fastq", "reads_1.fastq.gz": "reads.fastq.gz"}
+ for n in ("sequence.fasta", "reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"):
+ if n not in col:
+ continue
+ with col.open(n, 'rb') as qf:
+ tgt = qc_fasta(qf)[0]
+ if tgt != n and tgt != paired.get(n):
+ logging.info("Expected %s but magic says it should be %s", n, tgt)
+ valid = False
+ elif tgt in ("reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"):
+ start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid, n)
+ return False
+ if tgt is None:
+ valid = False
+ logging.warn("Upload '%s' does not contain sequence.fasta, reads.fastq or reads_1.fastq", collection["name"])
+ except ValueError as v:
valid = False
- logging.warn("Upload '%s' does not contain sequence.fasta, reads.fastq or reads_1.fastq", collection["name"])
dup = api.collections().list(filters=[["owner_uuid", "=", validated_project],
["portable_data_hash", "=", col.portable_data_hash()]]).execute()
@@ -70,9 +73,8 @@ def validate_upload(api, collection, validated_project,
"owner_uuid": validated_project,
"name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime()))}).execute()
else:
- pass
# It is invalid, delete it.
- #logging.warn("Deleting '%s'" % collection["name"])
+ logging.warn("Suggest deleting '%s'" % collection["name"])
#api.collections().delete(uuid=collection["uuid"]).execute()
return valid
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index 607c8c0..e198430 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -58,6 +58,9 @@ def qc_fasta(arg_sequence):
tmp1.write(submitlabel.encode("utf8"))
tmp1.write(("".join(submitseq)).encode("utf8"))
tmp1.flush()
+ subbp = 0
+ refbp = 0
+ similarity = 0
try:
cmd = ["clustalw", "-infile="+tmp1.name,
"-quicktree", "-iteration=none", "-type=DNA"]
@@ -78,12 +81,14 @@ def qc_fasta(arg_sequence):
except Exception as e:
logging.warn("Error trying to QC against reference sequence using 'clustalw': %s", e)
- if (subbp/refbp) < .7:
+ if refbp and (subbp/refbp) < .7:
raise ValueError("QC fail: submit sequence length is shorter than 70% reference")
- if (subbp/refbp) > 1.3:
+ if refbp and (subbp/refbp) > 1.3:
raise ValueError("QC fail: submit sequence length is greater than 130% reference")
- if similarity < 70.0:
+ if similarity and similarity < 70.0:
raise ValueError("QC fail: submit similarity is less than 70%")
+ if refbp == 0 or similarity == 0:
+ raise ValueError("QC fail")
return ("sequence.fasta"+gz, seqlabel)
elif seq_type == "text/fastq":