diff options
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/main.py | 29 | ||||
| -rw-r--r-- | bh20sequploader/qc_fasta.py | 73 | ||||
| -rw-r--r-- | bh20sequploader/qc_metadata.py | 21 |
3 files changed, 60 insertions, 63 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index c442af0..fd0278d 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -22,30 +22,32 @@ 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): + failed = False try: - log.debug("Checking metadata") - if not qc_metadata(metadata.name): + log.debug("Checking metadata" if do_qc else "Skipping metadata check") + if do_qc and not qc_metadata(metadata.name): log.warning("Failed metadata qc") - exit(1) - except ValueError as e: + failed = True + except Exception as e: log.debug(e) - log.debug("Failed metadata qc") print(e) - exit(1) + failed = True target = [] try: - log.debug("Checking FASTA/FASTQ QC") - target.append(qc_fasta(sequence_p1)) + log.debug("FASTA/FASTQ QC" if do_qc else "Limited FASTA/FASTQ QC") + 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]) target[1] = ("reads_2."+target[1][0][6:], target[0][1]) - except ValueError as e: + except Exception as e: log.debug(e) - log.debug("Failed FASTA qc") print(e) + failed = True + + if failed: exit(1) return target @@ -62,13 +64,14 @@ def main(): parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis') parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json') parser.add_argument('sequence_p1', type=argparse.FileType('rb'), help='sequence FASTA/FASTQ') - parser.add_argument('sequence_p2', type=argparse.FileType('rb'), default=None, help='sequence FASTQ pair') + 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 e198430..37eb4e8 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: @@ -51,47 +51,48 @@ def qc_fasta(arg_sequence): if seq_type == "text/fasta": # ensure that contains only one entry submitlabel, submitseq = read_fasta(sequence) + sequence.seek(0) + sequence.detach() - with tempfile.NamedTemporaryFile() as tmp1: - refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta") - tmp1.write(refstring) - 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"] - print("QC checking similarity to reference") - print(" ".join(cmd)) - result = subprocess.run(cmd, stdout=subprocess.PIPE) - res = result.stdout.decode("utf-8") - g1 = re.search(r"^Sequence 1: [^ ]+ +(\d+) bp$", res, flags=re.MULTILINE) - refbp = float(g1.group(1)) - g2 = re.search(r"^Sequence 2: [^ ]+ +(\d+) bp$", res, flags=re.MULTILINE) - subbp = float(g2.group(1)) - g3 = re.search(r"^Sequences \(1:2\) Aligned\. Score: (\d+(\.\d+)?)$", res, flags=re.MULTILINE) - similarity = float(g3.group(1)) + if not check_with_clustalw: + return ("sequence.fasta"+gz, seqlabel) - print(g1.group(0)) - 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) + with tempfile.NamedTemporaryFile() as tmp1: + with tempfile.NamedTemporaryFile() as tmp2: + refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta") + tmp1.write(refstring) + tmp1.flush() + tmp2.write(submitlabel.encode("utf8")) + tmp2.write(("".join(submitseq)).encode("utf8")) + tmp2.flush() + subbp = 0 + refbp = 0 + similarity = 0 + try: + cmd = ["minimap2", "-c", tmp1.name, tmp2.name] + logging.info("QC checking similarity to reference") + logging.info(" ".join(cmd)) + result = subprocess.run(cmd, stdout=subprocess.PIPE) + result.check_returncode() + res = result.stdout.decode("utf-8") + mm = res.split("\t") + if len(mm) >= 10: + # divide Number of matching bases in the mapping / Target sequence length + similarity = (float(mm[9]) / float(mm[6])) * 100.0 + else: + similarity = 0 + except Exception as e: + logging.warn("QC against reference sequence using 'minimap2': %s", e, exc_info=e) - if refbp and (subbp/refbp) < .7: - raise ValueError("QC fail: submit sequence length is shorter than 70% reference") - if refbp and (subbp/refbp) > 1.3: - raise ValueError("QC fail: submit sequence length is greater than 130% reference") - 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") + if similarity and similarity < 70.0: + raise ValueError("QC fail: alignment to reference was less than 70%% (was %2.2f%%)" % (similarity)) + if similarity == 0: + raise ValueError("QC fail") return ("sequence.fasta"+gz, seqlabel) elif seq_type == "text/fastq": + sequence.seek(0) + sequence.detach() return ("reads.fastq"+gz, seqlabel) else: raise ValueError("Sequence file does not look like a DNA FASTA or FASTQ") diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py index 9122ace..2b57991 100644 --- a/bh20sequploader/qc_metadata.py +++ b/bh20sequploader/qc_metadata.py @@ -21,20 +21,13 @@ def qc_metadata(metadatafile): shex = pkg_resources.resource_stream(__name__, "bh20seq-shex.rdf").read().decode("utf-8") if not isinstance(avsc_names, schema_salad.avro.schema.Names): - print(avsc_names) - return False + raise Exception(avsc_names) - try: - doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True) - g = schema_salad.jsonld_context.makerdf("workflow", doc, document_loader.ctx) - rslt, reason = evaluate(g, shex, doc["id"], "https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape") + doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True) + g = schema_salad.jsonld_context.makerdf("workflow", doc, document_loader.ctx) + rslt, reason = evaluate(g, shex, doc["id"], "https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape") - if not rslt: - log.debug(reason) - print(reason) + if not rslt: + raise Exception(reason) - return rslt - except Exception as e: - traceback.print_exc() - log.warn(e) - return False + return True |