From afbc3ec99f638a2f8df96a8e952b5b9616dc99a8 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Tue, 7 Apr 2020 13:31:49 -0400 Subject: Now moves collections into 'validated sequences' project Improve logging for seq service Fix uploader bug Runs workflow with all validated sequences. --- bh20sequploader/main.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'bh20sequploader') diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 17ad492..d3ebc0c 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -49,4 +49,5 @@ def main(): (properties['upload_user'], properties['upload_ip']), properties=properties, ensure_unique_name=True) -main() +if __name__ == "__main__": + main() -- cgit v1.2.3 From 40df65dec296b81650987c8ee4f832b703ab8f74 Mon Sep 17 00:00:00 2001 From: lltommy Date: Tue, 7 Apr 2020 19:51:49 +0200 Subject: adding dummy metadata qc to the project --- bh20sequploader/qc_metadata.py | 13 +++++++++++++ example/dummyschema.yaml | 16 ++++++++++++++++ example/metadata.json | 0 example/metadata.yaml | 17 +++++++++++++++++ 4 files changed, 46 insertions(+) create mode 100644 bh20sequploader/qc_metadata.py create mode 100644 example/dummyschema.yaml delete mode 100644 example/metadata.json create mode 100644 example/metadata.yaml (limited to 'bh20sequploader') diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py new file mode 100644 index 0000000..0632777 --- /dev/null +++ b/bh20sequploader/qc_metadata.py @@ -0,0 +1,13 @@ +import yamale + +## NOTE: this is just a DUMMY. Everything about this can and will change +def qc_metadata(metadatafile): + print("Start metadata validation...") + schema = yamale.make_schema('../example/dummyschema.yaml') + data = yamale.make_data(metadatafile) + # Validate data against the schema. Throws a ValueError if data is invalid. + yamale.validate(schema, data) + print("...complete!") + +#qc_metadata("../example/metadata.yaml") + diff --git a/example/dummyschema.yaml b/example/dummyschema.yaml new file mode 100644 index 0000000..e428324 --- /dev/null +++ b/example/dummyschema.yaml @@ -0,0 +1,16 @@ +#sampleInformation: include('sampleInformation') +#InstituteInformation: include('InstituteInformation') +--- +sampleInformation: + location : str() + host : str() + sequenceTechnology: str() + assemblyMethod: str() + +InstituteInformation: + OriginatingLab: str() + SubmittingLab: str() + +VirusDetail: + VirusName: str() + AccessionId: str() diff --git a/example/metadata.json b/example/metadata.json deleted file mode 100644 index e69de29..0000000 diff --git a/example/metadata.yaml b/example/metadata.yaml new file mode 100644 index 0000000..587d0be --- /dev/null +++ b/example/metadata.yaml @@ -0,0 +1,17 @@ +sampleInformation: + location: "USA" + host : "Homo Sapiens" + sequenceTechnology: "Sanger" + assemblyMethod: "CLC Genomics" + +InstituteInformation: + OriginatingLab: "Erik's kitchen" + SubmittingLab: "National Institute for Viral Disease Control and Prevention, China CDC" + +SubmitterInformation: + Submitter: "National Institute for Viral Disease Control and Prevention, China CDC" + submissionDate: "04-04-2020" + +VirusDetail: + VirusName: "hCoV-19/USA/identifer/2020" + AccessionId: "EPI_ISL_Random" -- cgit v1.2.3 From 07bc4c65535437b8e9e0744f08da8cea541d0116 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Tue, 7 Apr 2020 15:28:42 -0400 Subject: Add metadata validation with schema-salad --- bh20seqanalyzer/main.py | 11 ++++++++--- bh20sequploader/bh20seq-schema.yml | 36 ++++++++++++++++++++++++++++++++++++ bh20sequploader/main.py | 7 +++++-- bh20sequploader/qc_metadata.py | 26 +++++++++++++++++--------- example/dummyschema.yaml | 16 ---------------- setup.py | 3 ++- 6 files changed, 68 insertions(+), 31 deletions(-) create mode 100644 bh20sequploader/bh20seq-schema.yml delete mode 100644 example/dummyschema.yaml (limited to 'bh20sequploader') diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 2513ea3..78e32c9 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -6,12 +6,14 @@ import subprocess import tempfile import json import logging +import ruamel.yaml +from bh20sequploader.qc_metadata import qc_metadata logging.basicConfig(format="[%(asctime)s] %(levelname)s %(message)s", datefmt="%Y-%m-%d %H:%M:%S", level=logging.INFO) logging.getLogger("googleapiclient.discovery").setLevel(logging.WARN) -def validate_upload(api, collection, validated_project, latest_result_uuid): +def validate_upload(api, collection, validated_project): col = arvados.collection.Collection(collection["uuid"]) # validate the collection here. Check metadata, etc. @@ -20,9 +22,12 @@ def validate_upload(api, collection, validated_project, latest_result_uuid): if "sequence.fasta" not in col: valid = False logging.warn("Upload '%s' missing sequence.fasta", collection["name"]) - if "metadata.jsonld" not in col: - logging.warn("Upload '%s' missing metadata.jsonld", collection["name"]) + if "metadata.yaml" not in col: + logging.warn("Upload '%s' missing metadata.yaml", collection["name"]) valid = False + else: + metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml")) + valid = qc_metadata(metadata_content) and valid dup = api.collections().list(filters=[["owner_uuid", "=", validated_project], ["portable_data_hash", "=", col.portable_data_hash()]]).execute() diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml new file mode 100644 index 0000000..6e0973a --- /dev/null +++ b/bh20sequploader/bh20seq-schema.yml @@ -0,0 +1,36 @@ +$graph: + +- name: sampleInformationSchema + type: record + fields: + location: string + host: string + sequenceTechnology: string + assemblyMethod: string + +- name: InstituteInformationSchema + type: record + fields: + OriginatingLab: string + SubmittingLab: string + +- name: SubmitterInformationSchema + type: record + fields: + Submitter: string + submissionDate: string + +- name: VirusDetailSchema + type: record + fields: + VirusName: string + AccessionId: string + +- name: MainSchema + type: record + documentRoot: true + fields: + sampleInformation: sampleInformationSchema + InstituteInformation: InstituteInformationSchema + SubmitterInformation: SubmitterInformationSchema + VirusDetail: VirusDetailSchema diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index d3ebc0c..8b8fefe 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' @@ -19,6 +20,8 @@ def main(): api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) + qc_metadata(args.metadata.name) + col = arvados.collection.Collection(api_client=api) print("Reading FASTA") @@ -29,8 +32,8 @@ def main(): 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: diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py index 0632777..78b31b2 100644 --- a/bh20sequploader/qc_metadata.py +++ b/bh20sequploader/qc_metadata.py @@ -1,13 +1,21 @@ -import yamale +import schema_salad.schema +import logging +import pkg_resources -## NOTE: this is just a DUMMY. Everything about this can and will change def qc_metadata(metadatafile): - print("Start metadata validation...") - schema = yamale.make_schema('../example/dummyschema.yaml') - data = yamale.make_data(metadatafile) - # Validate data against the schema. Throws a ValueError if data is invalid. - yamale.validate(schema, data) - print("...complete!") + schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml") + cache = {"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml": schema_resource.read().decode("utf-8")} + (document_loader, + avsc_names, + schema_metadata, + metaschema_loader) = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache) -#qc_metadata("../example/metadata.yaml") + if not isinstance(avsc_names, schema_salad.avro.schema.Names): + print(avsc_names) + return False + try: + doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True) + return True + except: + return False diff --git a/example/dummyschema.yaml b/example/dummyschema.yaml deleted file mode 100644 index e428324..0000000 --- a/example/dummyschema.yaml +++ /dev/null @@ -1,16 +0,0 @@ -#sampleInformation: include('sampleInformation') -#InstituteInformation: include('InstituteInformation') ---- -sampleInformation: - location : str() - host : str() - sequenceTechnology: str() - assemblyMethod: str() - -InstituteInformation: - OriginatingLab: str() - SubmittingLab: str() - -VirusDetail: - VirusName: str() - AccessionId: str() diff --git a/setup.py b/setup.py index 0685d37..48c25aa 100644 --- a/setup.py +++ b/setup.py @@ -15,7 +15,7 @@ try: except ImportError: tagger = egg_info_cmd.egg_info -install_requires = ["arvados-python-client"] +install_requires = ["arvados-python-client", "schema-salad"] needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv) pytest_runner = ["pytest < 6", "pytest-runner < 5"] if needs_pytest else [] @@ -30,6 +30,7 @@ setup( author_email="peter.amstutz@curii.com", license="Apache 2.0", packages=["bh20sequploader", "bh20seqanalyzer"], + package_data={"bh20sequploader": ["bh20seq-schema.yml"]}, install_requires=install_requires, setup_requires=[] + pytest_runner, tests_require=["pytest<5"], -- cgit v1.2.3 From 9458ed33da08c787c4bb20af7b4108c93334b351 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 8 Apr 2020 17:41:19 -0400 Subject: Fastq now runs through fastq2fasta pipeline then gets added to pangenome analysis. --- bh20seqanalyzer/main.py | 141 ++++++++++++++++++++++++++++++----------- bh20sequploader/main.py | 14 +++- bh20sequploader/qc_metadata.py | 6 +- 3 files changed, 120 insertions(+), 41 deletions(-) (limited to 'bh20sequploader') diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 78e32c9..1a8965b 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -13,21 +13,30 @@ logging.basicConfig(format="[%(asctime)s] %(levelname)s %(message)s", datefmt="% level=logging.INFO) logging.getLogger("googleapiclient.discovery").setLevel(logging.WARN) -def validate_upload(api, collection, validated_project): +def validate_upload(api, collection, validated_project, + fastq_project, fastq_workflow_uuid): col = arvados.collection.Collection(collection["uuid"]) # validate the collection here. Check metadata, etc. valid = True - if "sequence.fasta" not in col: - valid = False - logging.warn("Upload '%s' missing sequence.fasta", collection["name"]) if "metadata.yaml" not in col: logging.warn("Upload '%s' missing metadata.yaml", collection["name"]) valid = False else: metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml")) - valid = qc_metadata(metadata_content) and valid + #valid = qc_metadata(metadata_content) and valid + if not valid: + logging.warn("Failed metadata qc") + + if valid: + if "sequence.fasta" not in col: + if "reads.fastq" in col: + start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid) + return False + else: + valid = False + logging.warn("Upload '%s' missing sequence.fasta", collection["name"]) dup = api.collections().list(filters=[["owner_uuid", "=", validated_project], ["portable_data_hash", "=", col.portable_data_hash()]]).execute() @@ -39,7 +48,9 @@ def validate_upload(api, collection, validated_project): if valid: logging.info("Added '%s' to validated sequences" % collection["name"]) # Move it to the "validated" project to be included in the next analysis - api.collections().update(uuid=collection["uuid"], body={"owner_uuid": validated_project}).execute() + api.collections().update(uuid=collection["uuid"], body={ + "owner_uuid": validated_project, + "name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime()))}).execute() else: # It is invalid, delete it. logging.warn("Deleting '%s'" % collection["name"]) @@ -47,28 +58,15 @@ def validate_upload(api, collection, validated_project): return valid -def start_analysis(api, - analysis_project, - workflow_uuid, - validated_project): +def run_workflow(api, parent_project, workflow_uuid, name, inputobj): project = api.groups().create(body={ "group_class": "project", - "name": "Pangenome analysis", - "owner_uuid": analysis_project, + "name": name, + "owner_uuid": parent_project, }, ensure_unique_name=True).execute() - validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", validated_project]]) - with tempfile.NamedTemporaryFile() as tmp: - inputobj = { - "inputReads": [] - } - for v in validated: - inputobj["inputReads"].append({ - "class": "File", - "location": "keep:%s/sequence.fasta" % v["portable_data_hash"] - }) tmp.write(json.dumps(inputobj, indent=2).encode('utf-8')) tmp.flush() cmd = ["arvados-cwl-runner", @@ -83,32 +81,95 @@ def start_analysis(api, if comp.returncode != 0: logging.error(comp.stderr.decode('utf-8')) + return project + + +def start_fastq_to_fasta(api, collection, + analysis_project, + fastq_workflow_uuid): + newproject = run_workflow(api, analysis_project, fastq_workflow_uuid, "FASTQ to FASTA", { + "fastq_forward": { + "class": "File", + "location": "keep:%s/reads.fastq" % collection["portable_data_hash"] + }, + "metadata": { + "class": "File", + "location": "keep:%s/metadata.yaml" % collection["portable_data_hash"] + }, + "ref_fasta": { + "class": "File", + "location": "keep:ffef6a3b77e5e04f8f62a7b6f67264d1+556/SARS-CoV2-NC_045512.2.fasta" + } + }) + api.collections().update(uuid=collection["uuid"], + body={"owner_uuid": newproject["uuid"]}).execute() + +def start_pangenome_analysis(api, + analysis_project, + pangenome_workflow_uuid, + validated_project): + validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", validated_project]]) + inputobj = { + "inputReads": [] + } + for v in validated: + inputobj["inputReads"].append({ + "class": "File", + "location": "keep:%s/sequence.fasta" % v["portable_data_hash"] + }) + run_workflow(api, analysis_project, pangenome_workflow_uuid, "Pangenome analysis", inputobj) + + +def get_workflow_output_from_project(api, uuid): + cr = api.container_requests().list(filters=[['owner_uuid', '=', uuid], + ["requesting_container_uuid", "=", None]]).execute() + if cr["items"] and cr["items"][0]["output_uuid"]: + return cr["items"][0] + else: + return None + def copy_most_recent_result(api, analysis_project, latest_result_uuid): most_recent_analysis = api.groups().list(filters=[['owner_uuid', '=', analysis_project]], order="created_at desc", limit=1).execute() for m in most_recent_analysis["items"]: - cr = api.container_requests().list(filters=[['owner_uuid', '=', m["uuid"]], - ["requesting_container_uuid", "=", None]]).execute() - if cr["items"] and cr["items"][0]["output_uuid"]: - wf = cr["items"][0] + wf = get_workflow_output_from_project(api, m["uuid"]) + if wf: src = api.collections().get(uuid=wf["output_uuid"]).execute() dst = api.collections().get(uuid=latest_result_uuid).execute() if src["portable_data_hash"] != dst["portable_data_hash"]: logging.info("Copying latest result from '%s' to %s", m["name"], latest_result_uuid) api.collections().update(uuid=latest_result_uuid, body={"manifest_text": src["manifest_text"], - "description": "latest result from %s %s" % (m["name"], wf["uuid"])}).execute() + "description": "Result from %s %s" % (m["name"], wf["uuid"])}).execute() break +def move_fastq_to_fasta_results(api, analysis_project, uploader_project): + projects = api.groups().list(filters=[['owner_uuid', '=', analysis_project], + ["properties.moved_output", "!=", True]], + order="created_at desc",).execute() + for p in projects["items"]: + wf = get_workflow_output_from_project(api, p["uuid"]) + if wf: + logging.info("Moving completed fastq2fasta result %s back to uploader project", wf["output_uuid"]) + api.collections().update(uuid=wf["output_uuid"], + body={"owner_uuid": uploader_project}).execute() + p["properties"]["moved_output"] = True + api.groups().update(uuid=p["uuid"], body={"properties": p["properties"]}).execute() + + def main(): parser = argparse.ArgumentParser(description='Analyze collections uploaded to a project') parser.add_argument('--uploader-project', type=str, default='lugli-j7d0g-n5clictpuvwk8aa', help='') - parser.add_argument('--analysis-project', type=str, default='lugli-j7d0g-y4k4uswcqi3ku56', help='') + parser.add_argument('--pangenome-analysis-project', type=str, default='lugli-j7d0g-y4k4uswcqi3ku56', help='') + parser.add_argument('--fastq-project', type=str, default='lugli-j7d0g-xcjxp4oox2u1w8u', help='') parser.add_argument('--validated-project', type=str, default='lugli-j7d0g-5ct8p1i1wrgyjvp', help='') - parser.add_argument('--workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='') - parser.add_argument('--latest-result-uuid', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='') + + parser.add_argument('--pangenome-workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='') + parser.add_argument('--fastq-workflow-uuid', type=str, default='lugli-7fd4e-2zp9q4jo5xpif9y', help='') + + parser.add_argument('--latest-result-collection', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='') args = parser.parse_args() api = arvados.api() @@ -116,16 +177,24 @@ def main(): logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project)) while True: + move_fastq_to_fasta_results(api, args.fastq_project, args.uploader_project) + new_collections = api.collections().list(filters=[['owner_uuid', '=', args.uploader_project]]).execute() at_least_one_new_valid_seq = False for c in new_collections["items"]: - at_least_one_new_valid_seq = validate_upload(api, c, args.validated_project) or at_least_one_new_valid_seq + at_least_one_new_valid_seq = validate_upload(api, c, + args.validated_project, + args.fastq_project, + args.fastq_workflow_uuid) or at_least_one_new_valid_seq if at_least_one_new_valid_seq: - start_analysis(api, args.analysis_project, - args.workflow_uuid, - args.validated_project) + start_pangenome_analysis(api, + args.pangenome_analysis_project, + args.pangenome_workflow_uuid, + args.validated_project) - copy_most_recent_result(api, args.analysis_project, args.latest_result_uuid) + copy_most_recent_result(api, + args.pangenome_analysis_project, + args.latest_result_collection) - time.sleep(10) + time.sleep(15) diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 8b8fefe..56cbe22 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -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() diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py index 78b31b2..ebe4dfc 100644 --- a/bh20sequploader/qc_metadata.py +++ b/bh20sequploader/qc_metadata.py @@ -1,6 +1,7 @@ import schema_salad.schema import logging import pkg_resources +import logging def qc_metadata(metadatafile): schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml") @@ -17,5 +18,6 @@ def qc_metadata(metadatafile): try: doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True) return True - except: - return False + except Exception as e: + logging.warn(e) + return False -- cgit v1.2.3 From d7498093d0f5e0db052ef88815d57c2648d09425 Mon Sep 17 00:00:00 2001 From: lltommy Date: Thu, 9 Apr 2020 14:34:54 +0200 Subject: Updating schema and examples. This is still work in progress but we get there --- bh20sequploader/bh20seq-schema.yml | 60 ++++++++++++++++++++++++++------------ example/metadata.yaml | 49 ++++++++++++++++++++++--------- example/minimal_example.yaml | 14 +++++++++ 3 files changed, 91 insertions(+), 32 deletions(-) create mode 100644 example/minimal_example.yaml (limited to 'bh20sequploader') diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 6e0973a..38cfb48 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -1,36 +1,60 @@ $graph: -- name: sampleInformationSchema +- name: hostSchema type: record fields: - location: string - host: string - sequenceTechnology: string - assemblyMethod: string + host_id: string + host_species: string + host_common_name: string? + host_sex: string? + host_age: int? + host_age_unit: string? + host_health_status: string? + host_treatment: string? + additional_host_information: string? -- name: InstituteInformationSchema +- name: sampleSchema type: record fields: - OriginatingLab: string - SubmittingLab: string + collector_name: string + collecting_institution: string + specimen_source: string? + collection_date: string? + collection_location: string? + sample_storage_conditions: string? + additional_collection_information: string? -- name: SubmitterInformationSchema +- name: virusSchema type: record fields: - Submitter: string - submissionDate: string + virus_species: string? + virus_strain: string? -- name: VirusDetailSchema +- name: technologySchema type: record fields: - VirusName: string - AccessionId: string + sample_sequencing_technology: string + sequence_assembly_method: string? + sequencing_coverage: string? + +- name: submitterSchema + type: record + fields: + submitter_name: string + submitter_address: string? + originating_lab: string + lab_address: string? + provider_sample_id: string? + submitter_sample_id: string? + authors: string? + submitter_id: string? - name: MainSchema type: record documentRoot: true fields: - sampleInformation: sampleInformationSchema - InstituteInformation: InstituteInformationSchema - SubmitterInformation: SubmitterInformationSchema - VirusDetail: VirusDetailSchema + host: hostSchema + sample: sampleSchema + virus: virusSchema? + technology: technologySchema + submitter: submitterSchema \ No newline at end of file diff --git a/example/metadata.yaml b/example/metadata.yaml index 587d0be..8a93379 100644 --- a/example/metadata.yaml +++ b/example/metadata.yaml @@ -1,17 +1,38 @@ -sampleInformation: - location: "USA" - host : "Homo Sapiens" - sequenceTechnology: "Sanger" - assemblyMethod: "CLC Genomics" +host: + host_id: XX1 + host_species: string + host_common_name: string + host_sex: string + host_age: 20 + host_age_unit: string + host_health_status: string + host_treatment: string + additional_host_information: string -InstituteInformation: - OriginatingLab: "Erik's kitchen" - SubmittingLab: "National Institute for Viral Disease Control and Prevention, China CDC" +sample: + collector_name: XXX + collecting_institution: XXX + specimen_source: XXX + collection_date: XXX + collection_location: XXX + sample_storage_conditions: XXX + additional_collection_information: XXX -SubmitterInformation: - Submitter: "National Institute for Viral Disease Control and Prevention, China CDC" - submissionDate: "04-04-2020" +virus: + virus_species: XX + virus_strain: XX -VirusDetail: - VirusName: "hCoV-19/USA/identifer/2020" - AccessionId: "EPI_ISL_Random" +technology: + sample_sequencing_technology: XX + sequence_assembly_method: XX + sequencing_coverage: 70x + +submitter: + submitter_name: tester + submitter_address: testerAdd + originating_lab: testLab + lab_address: labAdd + provider_sample_id: string + submitter_sample_id: string + authors: testAuthor + submitter_id: X12 \ No newline at end of file diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml new file mode 100644 index 0000000..201b080 --- /dev/null +++ b/example/minimal_example.yaml @@ -0,0 +1,14 @@ +host: + host_id: XX + host_species: string + +sample: + collector_name: XXX + collecting_institution: XXX + +technology: + sample_sequencing_technology: XX + +submitter: + submitter_name: tester + originating_lab: testLab \ No newline at end of file -- cgit v1.2.3 From deedb2ed7046bbe81136b8d9d1edc353984d356b Mon Sep 17 00:00:00 2001 From: lltommy Date: Thu, 9 Apr 2020 20:38:55 +0200 Subject: Adding functionality of turning keys into ontology terms (URI). This is work in progress - of course! --- bh20sequploader/bh20seq-schema.yml | 30 ++++++++++++++++++++++++------ 1 file changed, 24 insertions(+), 6 deletions(-) (limited to 'bh20sequploader') diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 38cfb48..fd9e854 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -3,14 +3,20 @@ $graph: - name: hostSchema type: record fields: + host_species: + type: string + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0000532 host_id: string - host_species: string host_common_name: string? host_sex: string? host_age: int? host_age_unit: string? host_health_status: string? - host_treatment: string? + host_treatment: + type: string? + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0000727 additional_host_information: string? - name: sampleSchema @@ -20,7 +26,10 @@ $graph: collecting_institution: string specimen_source: string? collection_date: string? - collection_location: string? + collection_location: + type: string? + jsonldPredicate: + _id: https://schema.org/fromLocation sample_storage_conditions: string? additional_collection_information: string? @@ -33,9 +42,18 @@ $graph: - name: technologySchema type: record fields: - sample_sequencing_technology: string - sequence_assembly_method: string? - sequencing_coverage: string? + sample_sequencing_technology: + type: string + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0000532 + sequence_assembly_method: + type: string? + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0002699 + sequencing_coverage: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/FLU_0000848 - name: submitterSchema type: record -- cgit v1.2.3 From dbe094a150d6c969b3d69f112b3538e6a87a74a2 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Thu, 9 Apr 2020 15:59:46 -0400 Subject: Add "sequencefile" for the metadata subject. --- bh20sequploader/bh20seq-schema.yml | 13 ++++++++++++- example/metadata.yaml | 2 +- 2 files changed, 13 insertions(+), 2 deletions(-) (limited to 'bh20sequploader') diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index fd9e854..5c962d1 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -1,3 +1,8 @@ +$base: http://biohackathon.org/bh20-seq-schema +$namespaces: + sch: https://schema.org/ + efo: http://www.ebi.ac.uk/efo/ + obo: http://purl.obolibrary.org/obo/ $graph: - name: hostSchema @@ -75,4 +80,10 @@ $graph: sample: sampleSchema virus: virusSchema? technology: technologySchema - submitter: submitterSchema \ No newline at end of file + submitter: submitterSchema + sequencefile: + doc: The subject (eg the fasta/fastq file) that this metadata describes + type: string? + jsonldPredicate: + _id: "@id" + _type: "@id" diff --git a/example/metadata.yaml b/example/metadata.yaml index 8a93379..41ff93e 100644 --- a/example/metadata.yaml +++ b/example/metadata.yaml @@ -35,4 +35,4 @@ submitter: provider_sample_id: string submitter_sample_id: string authors: testAuthor - submitter_id: X12 \ No newline at end of file + submitter_id: X12 -- cgit v1.2.3 From bf93a6a2fec690eee4bff4891469cd5947102b3a Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 9 Apr 2020 17:02:38 -0500 Subject: Moved Guix documentation into separate file (as it confused people ;) --- README.md | 21 +++++---------------- bh20sequploader/main.py | 2 +- doc/INSTALL.md | 31 +++++++++++++++++++++++++++++++ 3 files changed, 37 insertions(+), 17 deletions(-) create mode 100644 doc/INSTALL.md (limited to 'bh20sequploader') diff --git a/README.md b/README.md index a6fe052..3a8e5f0 100644 --- a/README.md +++ b/README.md @@ -122,19 +122,7 @@ It should print some instructions about how to use the uploader. ## Installation with GNU Guix -Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you even when you don't have root access on an Ubuntu system. - -1. **Set up and enter a container with the necessary dependencies.** After installing Guix as `~/opt/guix/bin/guix`, run: - -```sh -~/opt/guix/bin/guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs -``` - -2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief: - -```sh -pip3 install --user git+https://github.com/arvados/bh20-seq-resource.git@master -``` +For running/developing the uploader with GNU Guix see [INSTALL.md](./doc/INSTALL.md) # Usage @@ -148,7 +136,7 @@ bh20-seq-uploader example/sequence.fasta example/metadata.json All these uploaded sequences are being fed into a workflow to generate a [pangenome](https://academic.oup.com/bib/article/19/1/118/2566735) for the virus. You can replicate this workflow yourself. -Get your SARS-CoV-2 sequences from GenBank in `seqs.fa`, and then run: +An example is to get your SARS-CoV-2 sequences from GenBank in `seqs.fa`, and then run a series of commands ```sh minimap2 -cx asm20 -X seqs.fa seqs.fa >seqs.paf @@ -157,6 +145,7 @@ odgi build -g seqs.gfa -s -o seqs.odgi odgi viz -i seqs.odgi -o seqs.png -x 4000 -y 500 -R -P 5 ``` -For more information on building pangenome models, [see this wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes). - +Here we convert such a pipeline into the Common Workflow Language (CWL) and +sources can be found [here](https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate). +For more information on building pangenome models, [see this wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes). diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 56cbe22..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' diff --git a/doc/INSTALL.md b/doc/INSTALL.md new file mode 100644 index 0000000..c5c486c --- /dev/null +++ b/doc/INSTALL.md @@ -0,0 +1,31 @@ +# INSTALLATION + +Other options for running this tool. + +## GNU Guix + +Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you even when you don't have root access on an Ubuntu system. + +1. **Set up and enter a container with the necessary dependencies.** After installing Guix as `~/opt/guix/bin/guix`, run: + +```sh +~/opt/guix/bin/guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs +``` + +2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief: + +```sh +pip3 install --user schema-salad arvados-python-client +``` + +Pip installed the following modules + +``` +arvados-python-client-2.0.1 ciso8601-2.1.3 future-0.18.2 google-api-python-client-1.6.7 httplib2-0.17.1 oauth2client-4.1.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 rsa-4.0 ruamel.yaml-0.15.77 six-1.14.0 uritemplate-3.0.1 ws4py-0.5.1 +``` + +3. Run the tool directly with + +```sh +~/opt/guix/bin/guix environment guix --ad-hoc git python openssl python-pycurl nss-certs -- python3 bh20sequploader/main.py +``` -- cgit v1.2.3 From ddabd9390d2b221786ef58a6d85200eecf82ca2f Mon Sep 17 00:00:00 2001 From: lltommy Date: Fri, 10 Apr 2020 15:39:56 +0200 Subject: Updating schema and examples, including URIs --- bh20sequploader/bh20seq-schema.yml | 145 ++++++++++++++++++++++++++++++------- example/metadata.yaml | 4 + example/minimal_example.yaml | 6 +- 3 files changed, 128 insertions(+), 27 deletions(-) (limited to 'bh20sequploader') diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 5c962d1..cf9b015 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -3,6 +3,10 @@ $namespaces: sch: https://schema.org/ efo: http://www.ebi.ac.uk/efo/ obo: http://purl.obolibrary.org/obo/ + sio: http://semanticscience.org/resource/ + edam: http://edamontology.org/ + evs: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# + $graph: - name: hostSchema @@ -12,37 +16,93 @@ $graph: type: string jsonldPredicate: _id: http://www.ebi.ac.uk/efo/EFO_0000532 - host_id: string - host_common_name: string? - host_sex: string? - host_age: int? - host_age_unit: string? - host_health_status: string? + host_id: + type: string + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000115 + host_common_name: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NOMEN_0000037 + host_sex: + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/PATO_0000047 + host_age: + type: int? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/PATO_0000011 + host_age_unit: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/UO_0000036 + host_health_status: + type: string? + jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688 host_treatment: type: string? jsonldPredicate: _id: http://www.ebi.ac.uk/efo/EFO_0000727 - additional_host_information: string? + host_vaccination: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/VO_0000001 + additional_host_information: + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 - name: sampleSchema type: record fields: - collector_name: string - collecting_institution: string - specimen_source: string? - collection_date: string? + collector_name: + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0001895 + collecting_institution: + type: string + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 + specimen_source: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0001479 + collection_date: + type: string? + jsonldPredicate: + _id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164 collection_location: type: string? jsonldPredicate: - _id: https://schema.org/fromLocation - sample_storage_conditions: string? - additional_collection_information: string? + _id: http://purl.obolibrary.org/obo/GAZ_00000448 + sample_storage_conditions: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0001472 + additional_collection_information: + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 + sample_id: + type: string + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000115 + source_database_accession: + type: string? + jsonldPredicate: + _id: http://edamontology.org/data_2091 - name: virusSchema type: record fields: - virus_species: string? - virus_strain: string? + virus_species: + type: string? + jsonldPredicate: + _id: http://edamontology.org/data_1875 + virus_strain: + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_010055 - name: technologySchema type: record @@ -50,7 +110,7 @@ $graph: sample_sequencing_technology: type: string jsonldPredicate: - _id: http://www.ebi.ac.uk/efo/EFO_0000532 + _id: http://purl.obolibrary.org/obo/OBI_0600047 sequence_assembly_method: type: string? jsonldPredicate: @@ -63,14 +123,42 @@ $graph: - name: submitterSchema type: record fields: - submitter_name: string - submitter_address: string? - originating_lab: string - lab_address: string? - provider_sample_id: string? - submitter_sample_id: string? - authors: string? - submitter_id: string? + submitter_name: + type: string + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000116 + submitter_date: + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C94162 + submitter_address: + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000172 + originating_lab: + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C37984 + lab_address: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0600047 + provider_sample_id: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C37900 + submitter_sample_id: + type: string? + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0001741 + authors: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C42781 + submitter_id: + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000115 - name: MainSchema type: record @@ -81,9 +169,14 @@ $graph: virus: virusSchema? technology: technologySchema submitter: submitterSchema + submission: + type: string + jsonldPredicate: + _id: "@id" + #_type: "@id" sequencefile: doc: The subject (eg the fasta/fastq file) that this metadata describes type: string? jsonldPredicate: _id: "@id" - _type: "@id" + _type: "@id" \ No newline at end of file diff --git a/example/metadata.yaml b/example/metadata.yaml index 41ff93e..a2f6e57 100644 --- a/example/metadata.yaml +++ b/example/metadata.yaml @@ -1,3 +1,5 @@ +submission: publicSequenceResource + host: host_id: XX1 host_species: string @@ -10,6 +12,7 @@ host: additional_host_information: string sample: + sample_id: XXX collector_name: XXX collecting_institution: XXX specimen_source: XXX @@ -36,3 +39,4 @@ submitter: submitter_sample_id: string authors: testAuthor submitter_id: X12 + submitter_date: Subdate diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml index 201b080..f312ab7 100644 --- a/example/minimal_example.yaml +++ b/example/minimal_example.yaml @@ -1,8 +1,11 @@ +submission: publicSequenceResource + host: host_id: XX host_species: string sample: + sample_id: XXX collector_name: XXX collecting_institution: XXX @@ -11,4 +14,5 @@ technology: submitter: submitter_name: tester - originating_lab: testLab \ No newline at end of file + originating_lab: testLab + submitter_date: Subdate \ No newline at end of file -- cgit v1.2.3 From bef2a43185f9494398f5d5a8cdb6c5f34352f912 Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Fri, 10 Apr 2020 18:27:44 +0200 Subject: validate seq format with magic file --- bh20sequploader/main.py | 29 +++++++++++++++++++++++++---- bh20sequploader/validation/Makefile | 4 ++++ bh20sequploader/validation/formats | 4 ++++ bh20sequploader/validation/formats.mgc | Bin 0 -> 1032 bytes 4 files changed, 33 insertions(+), 4 deletions(-) create mode 100644 bh20sequploader/validation/Makefile create mode 100644 bh20sequploader/validation/formats create mode 100644 bh20sequploader/validation/formats.mgc (limited to 'bh20sequploader') diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index bf74ea5..1d5b9c3 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -3,6 +3,8 @@ import time import arvados import arvados.collection import json +import magic +from pathlib import Path import urllib.request import socket import getpass @@ -14,7 +16,7 @@ UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa' def main(): parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis') - parser.add_argument('sequence', type=argparse.FileType('r'), help='sequence FASTA') + parser.add_argument('sequence', type=argparse.FileType('r'), help='sequence FASTA/FASTQ') parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json') args = parser.parse_args() @@ -26,10 +28,27 @@ def main(): col = arvados.collection.Collection(api_client=api) - 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"): + magic_file = Path(__file__).parent / "validation" / "formats.mgc" + val = magic.Magic(magic_file=magic_file.resolve().as_posix(), + uncompress=False, mime=True) + seq_type = val.from_file(args.sequence.name).lower() + print(f"Sequence type: {seq_type}") + if seq_type == "text/fasta": + # ensure that contains only one entry + entries = 0 + for line in args.sequence: + if line.startswith(">"): + entries += 1 + if entries > 1: + raise ValueError("FASTA file contains multiple entries") + break + args.sequence.close() + args.sequence = open(args.sequence.name, "r") target = "reads.fastq" + elif seq_type == "text/fastq": + target = "sequence.fasta" + else: + raise ValueError("Sequence file does not look like FASTA or FASTQ") with col.open(target, "w") as f: r = args.sequence.read(65536) @@ -37,6 +56,7 @@ def main(): while r: f.write(r) r = args.sequence.read(65536) + args.sequence.close() print("Reading metadata") with col.open("metadata.yaml", "w") as f: @@ -45,6 +65,7 @@ def main(): while r: f.write(r) r = args.metadata.read(65536) + args.metadata.close() external_ip = urllib.request.urlopen('https://ident.me').read().decode('utf8') diff --git a/bh20sequploader/validation/Makefile b/bh20sequploader/validation/Makefile new file mode 100644 index 0000000..1ca13fb --- /dev/null +++ b/bh20sequploader/validation/Makefile @@ -0,0 +1,4 @@ +compile: formats.mgc + +formats.mgc : + file -C -m formats diff --git a/bh20sequploader/validation/formats b/bh20sequploader/validation/formats new file mode 100644 index 0000000..ac804cf --- /dev/null +++ b/bh20sequploader/validation/formats @@ -0,0 +1,4 @@ +0 regex \^\>.+\r?\n([acgtnACGTN]+\r?\n)*[acgtnACGTN]+(\r?\n)?$ FASTA +!:mime text/fasta +0 regex \^@.+\r?\n[acgtnACGTN]*\n\\+.*\n[!-i]*(\r\n)? FASTQ +!:mime text/fastq \ No newline at end of file diff --git a/bh20sequploader/validation/formats.mgc b/bh20sequploader/validation/formats.mgc new file mode 100644 index 0000000..bff282a Binary files /dev/null and b/bh20sequploader/validation/formats.mgc differ -- cgit v1.2.3 From 9b7fbc52ae229d72e75de9f433eea00ce37ba70a Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 10 Apr 2020 11:52:18 -0500 Subject: Fixed TypeError: 'module' object is not callable --- bh20sequploader/main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'bh20sequploader') diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index bf74ea5..ede9f38 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -6,7 +6,7 @@ import json import urllib.request import socket import getpass -import qc_metadata +from qc_metadata import qc_metadata ARVADOS_API_HOST='lugli.arvadosapi.com' ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' -- cgit v1.2.3 From a6ba9a5203a568611a94c043fd13e2ec50f071da Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Fri, 10 Apr 2020 15:12:08 -0400 Subject: Validate & propagate metadata --- bh20seqanalyzer/main.py | 45 ++++++++++++++++++++++++++++++++------ bh20sequploader/bh20seq-schema.yml | 6 ++--- bh20sequploader/main.py | 2 +- bh20sequploader/qc_metadata.py | 29 +++++++++++++++++++++++- 4 files changed, 70 insertions(+), 12 deletions(-) (limited to 'bh20sequploader') diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 2030c1e..1fb51b5 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -8,6 +8,8 @@ import json import logging import ruamel.yaml from bh20sequploader.qc_metadata import qc_metadata +import pkg_resources +from schema_salad.sourceline import add_lc_filename logging.basicConfig(format="[%(asctime)s] %(levelname)s %(message)s", datefmt="%Y-%m-%d %H:%M:%S", level=logging.INFO) @@ -24,8 +26,14 @@ def validate_upload(api, collection, validated_project, logging.warn("Upload '%s' missing metadata.yaml", collection["name"]) valid = False else: - metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml")) - #valid = qc_metadata(metadata_content) and valid + try: + metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml")) + metadata_content["id"] = "keep:%s/metadata.yaml" % collection["portable_data_hash"] + add_lc_filename(metadata_content, metadata_content["id"]) + valid = qc_metadata(metadata_content) and valid + except Exception as e: + logging.warn(e) + valid = False if not valid: logging.warn("Failed metadata qc") @@ -52,9 +60,10 @@ 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"]) - api.collections().delete(uuid=collection["uuid"]).execute() + #logging.warn("Deleting '%s'" % collection["name"]) + #api.collections().delete(uuid=collection["uuid"]).execute() return valid @@ -107,12 +116,17 @@ def start_fastq_to_fasta(api, collection, def start_pangenome_analysis(api, analysis_project, pangenome_workflow_uuid, - validated_project): + validated_project, + schema_ref): validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", validated_project]]) inputobj = { "inputReads": [], "metadata": [], - "subjects": [] + "subjects": [], + "metadataSchema": { + "class": "File", + "location": schema_ref + } } for v in validated: inputobj["inputReads"].append({ @@ -166,12 +180,26 @@ def move_fastq_to_fasta_results(api, analysis_project, uploader_project): api.groups().update(uuid=p["uuid"], body={"properties": p["properties"]}).execute() +def upload_schema(api, workflow_def_project): + schema_resource = pkg_resources.resource_stream('bh20sequploader.qc_metadata', "bh20seq-schema.yml") + c = arvados.collection.Collection() + with c.open("schema.yml", "wb") as f: + f.write(schema_resource.read()) + pdh = c.portable_data_hash() + wd = api.collections().list(filters=[["owner_uuid", "=", workflow_def_project], + ["portable_data_hash", "=", pdh]]).execute() + if len(wd["items"]) == 0: + c.save_new(owner_uuid=workflow_def_project, name="Metadata schema", ensure_unique_name=True) + return "keep:%s/schema.yml" % pdh + + def main(): parser = argparse.ArgumentParser(description='Analyze collections uploaded to a project') parser.add_argument('--uploader-project', type=str, default='lugli-j7d0g-n5clictpuvwk8aa', help='') parser.add_argument('--pangenome-analysis-project', type=str, default='lugli-j7d0g-y4k4uswcqi3ku56', help='') parser.add_argument('--fastq-project', type=str, default='lugli-j7d0g-xcjxp4oox2u1w8u', help='') parser.add_argument('--validated-project', type=str, default='lugli-j7d0g-5ct8p1i1wrgyjvp', help='') + parser.add_argument('--workflow-def-project', type=str, default='lugli-j7d0g-5hswinmpyho8dju', help='') parser.add_argument('--pangenome-workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='') parser.add_argument('--fastq-workflow-uuid', type=str, default='lugli-7fd4e-2zp9q4jo5xpif9y', help='') @@ -183,6 +211,8 @@ def main(): logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project)) + schema_ref = upload_schema(api, args.workflow_def_project) + while True: move_fastq_to_fasta_results(api, args.fastq_project, args.uploader_project) @@ -198,7 +228,8 @@ def main(): start_pangenome_analysis(api, args.pangenome_analysis_project, args.pangenome_workflow_uuid, - args.validated_project) + args.validated_project, + schema_ref) copy_most_recent_result(api, args.pangenome_analysis_project, diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index cf9b015..a072bd7 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -174,9 +174,9 @@ $graph: jsonldPredicate: _id: "@id" #_type: "@id" - sequencefile: - doc: The subject (eg the fasta/fastq file) that this metadata describes + id: + doc: The subject (eg the fasta/fastq file) that the metadata describes type: string? jsonldPredicate: _id: "@id" - _type: "@id" \ No newline at end of file + _type: "@id" diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index bfb8c51..2032508 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -22,7 +22,7 @@ def main(): api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) - if not qc_metadata(args.metadata.name): + if not bh20sequploader.qc_metadata.qc_metadata(args.metadata.name): print("Failed metadata qc") exit(1) diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py index ebe4dfc..38edcaa 100644 --- a/bh20sequploader/qc_metadata.py +++ b/bh20sequploader/qc_metadata.py @@ -1,12 +1,25 @@ import schema_salad.schema +import schema_salad.ref_resolver import logging import pkg_resources import logging +import traceback + +class CustomFetcher(schema_salad.ref_resolver.DefaultFetcher): + def check_exists(sup, url): + if url.startswith("keep:"): + return True + else: + return super().check_exists(url) + + def supported_schemes(self): # type: () -> List[str] + return ["file", "http", "https", "mailto", "keep"] + def qc_metadata(metadatafile): schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml") cache = {"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml": schema_resource.read().decode("utf-8")} - (document_loader, + (loader, avsc_names, schema_metadata, metaschema_loader) = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache) @@ -15,9 +28,23 @@ def qc_metadata(metadatafile): print(avsc_names) return False + document_loader = schema_salad.ref_resolver.Loader( + loader.ctx, + schemagraph=loader.graph, + foreign_properties=loader.foreign_properties, + idx=loader.idx, + cache=loader.cache, + fetcher_constructor=CustomFetcher, + skip_schemas=loader.skip_schemas, + url_fields=loader.url_fields, + allow_attachments=loader.allow_attachments, + session=loader.session, + ) + try: doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True) return True except Exception as e: + traceback.print_exc() logging.warn(e) return False -- cgit v1.2.3 From 925058d0b3db70803d322cc2a33801240899a20a Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Fri, 10 Apr 2020 15:52:37 -0400 Subject: Fix up fasta/fastq validation --- bh20seqanalyzer/main.py | 9 ++++++++- bh20sequploader/main.py | 29 +++++------------------------ setup.py | 5 +++-- 3 files changed, 16 insertions(+), 27 deletions(-) (limited to 'bh20sequploader') diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 1fb51b5..c05b402 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -8,6 +8,7 @@ import json import logging import ruamel.yaml from bh20sequploader.qc_metadata import qc_metadata +from bh20sequploader.qc_fasta import qc_fasta import pkg_resources from schema_salad.sourceline import add_lc_filename @@ -38,7 +39,13 @@ def validate_upload(api, collection, validated_project, logging.warn("Failed metadata qc") if valid: - if "sequence.fasta" not in col: + if "sequence.fasta" in col: + try: + qc_fasta(col.open("sequence.fasta")) + except Exception as e: + logging.warn(e) + valid = False + else: if "reads.fastq" in col: start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid) return False diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 2032508..4a225f6 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -8,7 +8,8 @@ from pathlib import Path import urllib.request import socket import getpass -from qc_metadata import qc_metadata +from .qc_metadata import qc_metadata +from .qc_fasta import qc_fasta ARVADOS_API_HOST='lugli.arvadosapi.com' ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' @@ -22,34 +23,14 @@ def main(): api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) - if not bh20sequploader.qc_metadata.qc_metadata(args.metadata.name): + target = qc_fasta(args.sequence) + + if not qc_metadata(args.metadata.name): print("Failed metadata qc") exit(1) col = arvados.collection.Collection(api_client=api) - magic_file = Path(__file__).parent / "validation" / "formats.mgc" - val = magic.Magic(magic_file=magic_file.resolve().as_posix(), - uncompress=False, mime=True) - seq_type = val.from_file(args.sequence.name).lower() - print(f"Sequence type: {seq_type}") - if seq_type == "text/fasta": - # ensure that contains only one entry - entries = 0 - for line in args.sequence: - if line.startswith(">"): - entries += 1 - if entries > 1: - raise ValueError("FASTA file contains multiple entries") - break - args.sequence.close() - args.sequence = open(args.sequence.name, "r") - target = "reads.fastq" - elif seq_type == "text/fastq": - target = "sequence.fasta" - else: - raise ValueError("Sequence file does not look like FASTA or FASTQ") - with col.open(target, "w") as f: r = args.sequence.read(65536) print(r[0:20]) diff --git a/setup.py b/setup.py index 41ace7b..18e858e 100644 --- a/setup.py +++ b/setup.py @@ -15,7 +15,7 @@ try: except ImportError: tagger = egg_info_cmd.egg_info -install_requires = ["arvados-python-client", "schema-salad"] +install_requires = ["arvados-python-client", "schema-salad", "python-magic"] web_requires = ["flask", "pyyaml"] needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv) @@ -31,7 +31,8 @@ setup( author_email="peter.amstutz@curii.com", license="Apache 2.0", packages=["bh20sequploader", "bh20seqanalyzer", "bh20simplewebuploader"], - package_data={"bh20sequploader": ["bh20seq-schema.yml"]}, + package_data={"bh20sequploader": ["bh20seq-schema.yml", "validation/formats"], + }, install_requires=install_requires, extras_require={ 'web': web_requires -- cgit v1.2.3 From 1f66b8270a7bf06f98e2a336385bc84b778ead66 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Fri, 10 Apr 2020 15:53:58 -0400 Subject: Add qc_fasta --- bh20sequploader/qc_fasta.py | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 bh20sequploader/qc_fasta.py (limited to 'bh20sequploader') diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py new file mode 100644 index 0000000..e3d4fe7 --- /dev/null +++ b/bh20sequploader/qc_fasta.py @@ -0,0 +1,28 @@ +import pkg_resources +import tempfile +import magic + +def qc_fasta(sequence): + schema_resource = pkg_resources.resource_stream(__name__, "validation/formats") + with tempfile.NamedTemporaryFile() as tmp: + tmp.write(schema_resource.read()) + tmp.flush() + val = magic.Magic(magic_file=tmp.name, + uncompress=False, mime=True) + seq_type = val.from_buffer(sequence.read(4096)).lower() + sequence.seek(0) + if seq_type == "text/fasta": + # ensure that contains only one entry + entries = 0 + for line in sequence: + if line.startswith(">"): + entries += 1 + if entries > 1: + raise ValueError("FASTA file contains multiple entries") + break + sequence.seek(0) + return "reads.fastq" + elif seq_type == "text/fastq": + return "sequence.fasta" + else: + raise ValueError("Sequence file does not look like FASTA or FASTQ") -- cgit v1.2.3 From 1b1283131f3c684bfff2c1b165565957ac01b4be Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Fri, 10 Apr 2020 16:11:29 -0400 Subject: Fix swapped fasta/fastq Replace example sequence with COV19 reference instead of HIV. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- bh20seqanalyzer/main.py | 1 + bh20sequploader/qc_fasta.py | 4 +- example/sequence.fasta | 642 +++++++++++++++++++++++++++++--------------- 3 files changed, 432 insertions(+), 215 deletions(-) (limited to 'bh20sequploader') diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index c05b402..7626662 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -47,6 +47,7 @@ def validate_upload(api, collection, validated_project, valid = False else: if "reads.fastq" in col: + logging.info("Upload '%s' running fastq2fasta", collection["name"]) start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid) return False else: diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py index e3d4fe7..e47d66b 100644 --- a/bh20sequploader/qc_fasta.py +++ b/bh20sequploader/qc_fasta.py @@ -21,8 +21,8 @@ def qc_fasta(sequence): raise ValueError("FASTA file contains multiple entries") break sequence.seek(0) - return "reads.fastq" - elif seq_type == "text/fastq": return "sequence.fasta" + elif seq_type == "text/fastq": + return "reads.fastq" else: raise ValueError("Sequence file does not look like FASTA or FASTQ") diff --git a/example/sequence.fasta b/example/sequence.fasta index 3c4c0ef..b364687 100644 --- a/example/sequence.fasta +++ b/example/sequence.fasta @@ -1,214 +1,430 @@ ->AF324493.2 HIV-1 vector pNL4-3, complete sequence -TGGAAGGGCTAATTTGGTCCCAAAAAAGACAAGAGATCCTTGATCTGTGGATCTACCACACACAAGGCTA -CTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTTC -AAGTTAGTACCAGTTGAACCAGAGCAAGTAGAAGAGGCCAATGAAGGAGAGAACAACAGCTTGTTACACC -CTATGAGCCAGCATGGGATGGAGGACCCGGAGGGAGAAGTATTAGTGTGGAAGTTTGACAGCCTCCTAGC -ATTTCGTCACATGGCCCGAGAGCTGCATCCGGAGTACTACAAAGACTGCTGACATCGAGCTTTCTACAAG -GGACTTTCCGCTGGGGACTTTCCAGGGAGGTGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGAT -GCTACATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGC -TCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTCAAAGTAGTGTG -TGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCT -AGCAGTGGCGCCCGAACAGGGACTTGAAAGCGAAAGTAAAGCCAGAGGAGATCTCTCGACGCAGGACTCG -GCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGC -GGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCGGTATTAAGCGGGGGAGAATTAGATAAATGGGAA -AAAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAACTAAAACATATAGTATGGGCAAGCAGGGAGC -TAGAACGATTCGCAGTTAATCCTGGCCTTTTAGAGACATCAGAAGGCTGTAGACAAATACTGGGACAGCT -ACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAATAGCAGTCCTCTATTGT -GTGCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCCTTAGATAAGATAGAGGAAGAGCAAAACAAAA -GTAAGAAAAAGGCACAGCAAGCAGCAGCTGACACAGGAAACAACAGCCAGGTCAGCCAAAATTACCCTAT -AGTGCAGAACCTCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAA -GTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCC -CACAAGATTTAAATACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGAC -CATCAATGAGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAG -ATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGA -CACATAATCCACCTATCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGT -AAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTA -GACCGATTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAAGAGGTAAAAAATTGGATGACAGAAACCT -TGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGGAGCGACACTAGA -AGAAATGATGACAGCATGTCAGGGAGTGGGGGGACCCGGCCATAAAGCAAGAGTTTTGGCTGAAGCAATG -AGCCAAGTAACAAATCCAGCTACCATAATGATACAGAAAGGCAATTTTAGGAACCAAAGAAAGACTGTTA -AGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTG -GAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATC -TGGCCTTCCCACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAG -AGAGCTTCAGGTTTGGGGAAGAGACAACAACTCCCTCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTA -TCCTTTAGCTTCCCTCAGATCACTCTTTGGCAGCGACCCCTCGTCACAATAAAGATAGGGGGGCAATTAA -AGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGAAGATGGAA -ACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATC -TGCGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGT -TGACTCAGATTGGCTGCACTTTAAATTTTCCCATTAGTCCTATTGAGACTGTACCAGTAAAATTAAAGCC -AGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATT -TGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTAT -TTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAAC -TCAAGATTTCTGGGAAGTTCAATTAGGAATACCACATCCTGCAGGGTTAAAACAGAAAAAATCAGTAACA -GTACTGGATGTGGGCGATGCATATTTTTCAGTTCCCTTAGATAAAGACTTCAGGAAGTATACTGCATTTA -CCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAA -AGGATCACCAGCAATATTCCAGTGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGAC -ATAGTCATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAA -AAATAGAGGAACTGAGACAACATCTGTTGAGGTGGGGATTTACCACACCAGACAAAAAACATCAGAAAGA -ACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCA -GAAAAGGACAGCTGGACTGTCAATGACATACAGAAATTAGTGGGAAAATTGAATTGGGCAAGTCAGATTT -ATGCAGGGATTAAAGTAAGGCAATTATGTAAACTTCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACC -ACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAACCGGTACATGGAGTG -TATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAA -TTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAGTATGCAAGAATGAAGGGTGCCCACACTAATGA -TGTGAAACAATTAACAGAGGCAGTACAAAAAATAGCCACAGAAAGCATAGTAATATGGGGAAAGACTCCT -AAATTTAAATTACCCATACAAAAGGAAACATGGGAAGCATGGTGGACAGAGTATTGGCAAGCCACCTGGA -TTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTGAAGTTATGGTACCAGTTAGAGAAAGAACCCAT -AATAGGAGCAGAAACTTTCTATGTAGATGGGGCAGCCAATAGGGAAACTAAATTAGGAAAAGCAGGATAT -GTAACTGACAGAGGAAGACAAAAAGTTGTCCCCCTAACGGACACAACAAATCAGAAGACTGAGTTACAAG -CAATTCATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTGACAGACTCACAATATGCATTGGG -AATCATTCAAGCACAACCAGATAAGAGTGAATCAGAGTTAGTCAGTCAAATAATAGAGCAGTTAATAAAA -AAGGAAAAAGTCTACCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAAT -TGGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGAAGAACATGAGAA -ATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTACCACCTGTAGTAGCAAAAGAAATAGTA -GCCAGCTGTGATAAATGTCAGCTAAAAGGGGAAGCCATGCATGGACAAGTAGACTGTAGCCCAGGAATAT -GGCAGCTAGATTGTACACATTTAGAAGGAAAAGTTATCTTGGTAGCAGTTCATGTAGCCAGTGGATATAT -AGAAGCAGAAGTAATTCCAGCAGAGACAGGGCAAGAAACAGCATACTTCCTCTTAAAATTAGCAGGAAGA -TGGCCAGTAAAAACAGTACATACAGACAATGGCAGCAATTTCACCAGTACTACAGTTAAGGCCGCCTGTT -GGTGGGCGGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAATAGAATCTAT -GAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAA -ATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAG -TAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCG -GGTTTATTACAGGGACAGCAGAGATCCAGTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGG -GCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATCAGGGATT -ATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAACACATGGAAAAGAT -TAGTAAAACACCATATGTATATTTCAAGGAAAGCTAAGGACTGGTTTTATAGACATCACTATGAAAGTAC -TAATCCAAAAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAAATTAGTAATAACAACATATTGG -GGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGAT -ATAGCACACAAGTAGACCCTGACCTAGCAGACCAACTAATTCATCTGCACTATTTTGATTGTTTTTCAGA -ATCTGCTATAAGAAATACCATATTAGGACGTATAGTTAGTCCTAGGTGTGAATATCAAGCAGGACATAAC -AAGGTAGGATCTCTACAGTACTTGGCACTAGCAGCATTAATAAAACCAAAACAGATAAAGCCACCTTTGC -CTAGTGTTAGGAAACTGACAGAGGACAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCA -TACAATGAATGGACACTAGAGCTTTTAGAGGAACTTAAGAGTGAAGCTGTTAGACATTTTCCTAGGATAT -GGCTCCATAACTTAGGACAACATATCTATGAAACTTACGGGGATACTTGGGCAGGAGTGGAAGCCATAAT -AAGAATTCTGCAACAACTGCTGTTTATCCATTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACT -CGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAG -CCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATGACAA -AAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGAC -TCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATAATAGTAGCAATAGTAGCA -TTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAA -GACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGA -AGGAGAAGTATCAGCACTTGTGGAGATGGGGGTGGAAATGGGGCACCATGCTCCTTGGGATATTGATGAT -CTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACC -ACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCT -GTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAA -AAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTA -AAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTA -GCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGA -TAAGGTGCAGAAAGAATATGCATTCTTTTATAAACTTGATATAGTACCAATAGATAATACCAGCTATAGG -TTGATAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATAC -ATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATG -TACAAATGTCAGCACAGTACAATGTACACATGGAATCAGGCCAGTAGTATCAACTCAACTGCTGTTAAAT -GGCAGTCTAGCAGAAGAAGATGTAGTAATTAGATCTGCCAATTTCACAGACAATGCTAAAACCATAATAG -TACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATCCGTAT -CCAGAGGGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAAC -ATTAGTAGAGCAAAATGGAATGCCACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATA -ATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGG -AGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACT -GAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACACTCCCATGCAGAATAAAACAATTTATAAACA -TGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATAT -TACTGGGCTGCTATTAACAAGAGATGGTGGTAATAACAACAATGGGTCCGAGATCTTCAGACCTGGAGGA -GGCGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAG -TAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTT -CCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGGCCAGA -CAATTATTGTCTGATATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGT -TGCAACTCACAGTCTGGGGCATCAAACAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGA -TCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCT -AGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATAACATGACCTGGATGGAGTGGGACAGAGAAATTA -ACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGA -ATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATA -AAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGA -ATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAATCCCGAGGGGACCCGACAG -GCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC -TTAGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCT -TGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCT -CCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAACTTGCTCAATGCCACAGCCATAGCAGTA -GCTGAGGGGACAGATAGGGTTATAGAAGTATTACAAGCAGCTTATAGAGCTATTCGCCACATACCTAGAA -GAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTG -GATGGCCTGCTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATGGGGTGGGAGCAGTATCTCG -AGACCTAGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTAACAATGCTGCTTGTGCCTGGCTA -GAAGCACAAGAGGAGGAAGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACA -AGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAG -AAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACA -CCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATA -AGGTAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGA -CCCTGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTG -CATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAG -GGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATGCTGCATATAAGCAGCTGCTTTTTG -CCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACT -GCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGT -AACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCACCCAGGAGGTAGAGGTTGCAG -TGAGCCAAGATCGCGCCACTGCATTCCAGCCTGGGCAAGAAAACAAGACTGTCTAAAATAATAATAATAA -GTTAAGGGTATTAAATATATTTATACATGGAGGTCATAAAAATATATATATTTGGGCTGGGCGCAGTGGC -TCACACCTGCGCCCGGCCCTTTGGGAGGCCGAGGCAGGTGGATCACCTGAGTTTGGGAGTTCCAGACCAG -CCTGACCAACATGGAGAAACCCCTTCTCTGTGTATTTTTAGTAGATTTTATTTTATGTGTATTTTATTCA -CAGGTATTTCTGGAAAACTGAAACTGTTTTTCCTCTACTCTGATACCACAAGAATCATCAGCACAGAGGA -AGACTTCTGTGATCAAATGTGGTGGGAGAGGGAGGTTTTCACCAGCACATGAGCAGTCAGTTCTGCCGCA -GACTCGGCGGGTGTCCTTCGGTTCAGTTCCAACACCGCCTGCCTGGAGAGAGGTCAGACCACAGGGTGAG -GGCTCAGTCCCCAAGACATAAACACCCAAGACATAAACACCCAACAGGTCCACCCCGCCTGCTGCCCAGG -CAGAGCCGATTCACCAAGACGGGAATTAGGATAGAGAAAGAGTAAGTCACACAGAGCCGGCTGTGCGGGA -GAACGGAGTTCTATTATGACTCAAATCAGTCTCCCCAAGCATTCGGGGATCAGAGTTTTTAAGGATAACT -TAGTGTGTAGGGGGCCAGTGAGTTGGAGATGAAAGCGTAGGGAGTCGAAGGTGTCCTTTTGCGCCGAGTC -AGTTCCTGGGTGGGGGCCACAAGATCGGATGAGCCAGTTTATCAATCCGGGGGTGCCAGCTGATCCATGG -AGTGCAGGGTCTGCAAAATATCTCAAGCACTGATTGATCTTAGGTTTTACAATAGTGATGTTACCCCAGG -AACAATTTGGGGAAGGTCAGAATCTTGTAGCCTGTAGCTGCATGACTCCTAAACCATAATTTCTTTTTTG -TTTTTTTTTTTTTATTTTTGAGACAGGGTCTCACTCTGTCACCTAGGCTGGAGTGCAGTGGTGCAATCAC -AGCTCACTGCAGCCTCAACGTCGTAAGCTCAAGCGATCCTCCCACCTCAGCCTGCCTGGTAGCTGAGACT -ACAAGCGACGCCCCAGTTAATTTTTGTATTTTTGGTAGAGGCAGCGTTTTGCCGTGTGGCCCTGGCTGGT -CTCGAACTCCTGGGCTCAAGTGATCCAGCCTCAGCCTCCCAAAGTGCTGGGACAACCGGGGCCAGTCACT -GCACCTGGCCCTAAACCATAATTTCTAATCTTTTGGCTAATTTGTTAGTCCTACAAAGGCAGTCTAGTCC -CCAGGCAAAAAGGGGGTTTGTTTCGGGAAAGGGCTGTTACTGTCTTTGTTTCAAACTATAAACTAAGTTC -CTCCTAAACTTAGTTCGGCCTACACCCAGGAATGAACAAGGAGAGCTTGGAGGTTAGAAGCACGATGGAA -TTGGTTAGGTCAGATCTCTTTCACTGTCTGAGTTATAATTTTGCAATGGTGGTTCAAAGACTGCCCGCTT -CTGACACCAGTCGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCT -TCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAA -AGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCA -AAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCAT -CACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCC -CTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCC -TTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCC -AAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTG -AGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAG -GTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTT -GGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAA -CCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGA -AGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTC -ATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAA -GTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTG -TCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCA -TCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACC -AGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTG -TTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGC -ATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTA -CATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTT -GGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGA -TGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCT -CTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAA -ACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGT -GCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAA -ATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTA -TTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAA -ATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACAT -TAACCTATAAAAATAGGCGTATCACGAGGCCCTTTCGTCTCGCGCGTTTCGGTGATGACGGTGAAAACCT -CTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGT -CAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCTGGCTTAACTATGCGGCATCAGAGCAGATTGTAC -TGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCCA -TTCGCCATTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGGGG -AGGCAGAGATTGCAGTAAGCTGAGATCGCAGCACTGCACTCCAGCCTGGGCGACAGAGTAAGACTCTGTC -TCAAAAATAAAATAAATAAATCAATCAGATATTCCAATCTTTTCCTTTATTTATTTATTTATTTTCTATT -TTGGAAACACAGTCCTTCCTTATTCCAGAATTACACATATATTCTATTTTTCTTTATATGCTCCAGTTTT -TTTTAGACCTTCACCTGAAATGTGTGTATACAAAATCTAGGCCAGTCCAGCAGAGCCTAAAGGTAAAAAA -TAAAATAATAAAAAATAAATAAAATCTAGCTCACTCCTTCACATCAAAATGGAGATACAGCTGTTAGCAT -TAAATACCAAATAACCCATCTTGTCCTCAATAATTTTAAGCGCCTCTCTCCACCACATCTAACTCCTGTC -AAAGGCATGTGCCCCTTCCGGGCGCTCTGCTGTGCTGCCAACCAACTGGCATGTGGACTCTGCAGGGTCC -CTAACTGCCAAGCCCCACAGTGTGCCCTGAGGCTGCCCCTTCCTTCTAGCGGCTGCCCCCACTCGGCTTT -GCTTTCCCTAGTTTCAGTTACTTGCGTTCAGCCAAGGTCTGAAACTAGGTGCGCACAGAGCGGTAAGACT -GCGAGAGAAAGAGACCAGCTTTACAGGGGGTTTATCACAGTGCACCCTGACAGTCGTCAGCCTCACAGGG -GGTTTATCACATTGCACCCTGACAGTCGTCAGCCTCACAGGGGGTTTATCACAGTGCACCCTTACAATCA -TTCCATTTGATTCACAATTTTTTTAGTCTCTACTGTGCCTAACTTGTAAGTTAAATTTGATCAGAGGTGT -GTTCCCAGAGGGGAAAACAGTATATACAGGGTTCAGTACTATCGCATTTCAGGCCTCCACCTGGGTCTTG -GAATGTGTCCCCCGAGGGGTGATGACTACCTCAGTTGGATCTCCACAGGTCACAGTGACACAAGATAACC -AAGACACCTCCCAAGGCTACCACAATGGGCCGCCCTCCACGTGCACATGGCCGGAGGAACTGCCATGTCG -GAGGTGCAAGCACACCTGCGCATCAGAGTCCTTGGTGTGGAGGGAGGGACCAGCGCAGCTTCCAGCCATC -CACCTGATGAACAGAACCTAGGGAAAGCCCCAGTTCTACTTACACCAGGAAAGGC +>NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome +ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA +CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC +TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG +TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC +CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC +GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG +CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT +GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC +GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT +TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA +GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG +TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG +CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG +TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG +CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA +ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA +CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC +CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA +GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT +ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG +GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG +CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA +CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA +ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA +GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT +TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG +GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG +TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC +GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG +ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG +GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT +AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA +TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT +AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA +GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC +TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT +AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA +GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT +ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA +GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT +GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA +ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC +ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA +TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG +AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT +TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA +CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC +AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT +AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA +GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA +CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG +TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT +GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT +TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAA +TGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGT +GAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTA +AACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAAGCTTGTGTTGAAGAAGTTACAACAAC +TCTGGAAGAAACTAAGTTCCTCACAGAAAACTTGTTACTTTATATTGACATTAATGGCAATCTTCATCCA +GATTCTGCCACTCTTGTTAGTGACATTGACATCACTTTCTTAAAGAAAGATGCTCCATATATAGTGGGTG +ATGTTGTTCAAGAGGGTGTTTTAACTGCTGTGGTTATACCTACTAAAAAGGCTGGTGGCACTACTGAAAT +GCTAGCGAAAGCTTTGAGAAAAGTGCCAACAGACAATTATATAACCACTTACCCGGGTCAGGGTTTAAAT +GGTTACACTGTAGAGGAGGCAAAGACAGTGCTTAAAAAGTGTAAAAGTGCCTTTTACATTCTACCATCTA +TTATCTCTAATGAGAAGCAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGC +AGAAGAAACACGCAAATTAATGCCTGTCTGTGTGGAAACTAAAGCCATAGTTTCAACTATACAGCGTAAA +TATAAGGGTATTAAAATACAAGAGGGTGTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAA +CAACTGTAGCGTCACTTATCAACACACTTAACGATCTAAATGAAACTCTTGTTACAATGCCACTTGGCTA +TGTAACACATGGCTTAAATTTGGAAGAAGCTGCTCGGTATATGAGATCTCTCAAAGTGCCAGCTACAGTT +TCTGTTTCTTCACCTGATGCTGTTACAGCGTATAATGGTTATCTTACTTCTTCTTCTAAAACACCTGAAG +AACATTTTATTGAAACCATCTCACTTGCTGGTTCCTATAAAGATTGGTCCTATTCTGGACAATCTACACA +ACTAGGTATAGAATTTCTTAAGAGAGGTGATAAAAGTGTATATTACACTAGTAATCCTACCACATTCCAC +CTAGATGGTGAAGTTATCACCTTTGACAATCTTAAGACACTTCTTTCTTTGAGAGAAGTGAGGACTATTA +AGGTGTTTACAACAGTAGACAACATTAACCTCCACACGCAAGTTGTGGACATGTCAATGACATATGGACA +ACAGTTTGGTCCAACTTATTTGGATGGAGCTGATGTTACTAAAATAAAACCTCATAATTCACATGAAGGT +AAAACATTTTATGTTTTACCTAATGATGACACTCTACGTGTTGAGGCTTTTGAGTACTACCACACAACTG +ATCCTAGTTTTCTGGGTAGGTACATGTCAGCATTAAATCACACTAAAAAGTGGAAATACCCACAAGTTAA +TGGTTTAACTTCTATTAAATGGGCAGATAACAACTGTTATCTTGCCACTGCATTGTTAACACTCCAACAA +ATAGAGTTGAAGTTTAATCCACCTGCTCTACAAGATGCTTATTACAGAGCAAGGGCTGGTGAAGCTGCTA +ACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAAT +GAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGT +GGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTACATGGGCACACTTTCTTATGAACAAT +TTAAGAAAGGTGTTCAGATACCTTGTACGTGTGGTAAACAAGCTACAAAATATCTAGTACAACAGGAGTC +ACCTTTTGTTATGATGTCAGCACCACCTGCTCAGTATGAACTTAAGCATGGTACATTTACTTGTGCTAGT +GAGTACACTGGTAATTACCAGTGTGGTCACTATAAACATATAACTTCTAAAGAAACTTTGTATTGCATAG +ACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAG +TTACACAACAACCATAAAACCAGTTACTTATAAATTGGATGGTGTTGTTTGTACAGAAATTGACCCTAAG +TTGGACAATTATTATAAGAAAGACAATTCTTATTTCACAGAGCAACCAATTGATCTTGTACCAAACCAAC +CATATCCAAACGCAAGCTTCGATAATTTTAAGTTTGTATGTGATAATATCAAATTTGCTGATGATTTAAA +CCAGTTAACTGGTTATAAGAAACCTGCTTCAAGAGAGCTTAAAGTTACATTTTTCCCTGACTTAAATGGT +GATGTGGTGGCTATTGATTATAAACACTACACACCCTCTTTTAAGAAAGGAGCTAAATTGTTACATAAAC +CTATTGTTTGGCATGTTAACAATGCAACTAATAAAGCCACGTATAAACCAAATACCTGGTGTATACGTTG +TCTTTGGAGCACAAAACCAGTTGAAACATCAAATTCGTTTGATGTACTGAAGTCAGAGGACGCGCAGGGA +ATGGATAATCTTGCCTGCGAAGATCTAAAACCAGTCTCTGAAGAAGTAGTGGAAAATCCTACCATACAGA +AAGACGTTCTTGAGTGTAATGTGAAAACTACCGAAGTTGTAGGAGACATTATACTTAAACCAGCAAATAA +TAGTTTAAAAATTACAGAAGAGGTTGGCCACACAGATCTAATGGCTGCTTATGTAGACAATTCTAGTCTT +ACTATTAAGAAACCTAATGAATTATCTAGAGTATTAGGTTTGAAAACCCTTGCTACTCATGGTTTAGCTG +CTGTTAATAGTGTCCCTTGGGATACTATAGCTAATTATGCTAAGCCTTTTCTTAACAAAGTTGTTAGTAC +AACTACTAACATAGTTACACGGTGTTTAAACCGTGTTTGTACTAATTATATGCCTTATTTCTTTACTTTA +TTGCTACAATTGTGTACTTTTACTAGAAGTACAAATTCTAGAATTAAAGCATCTATGCCGACTACTATAG +CAAAGAATACTGTTAAGAGTGTCGGTAAATTTTGTCTAGAGGCTTCATTTAATTATTTGAAGTCACCTAA +TTTTTCTAAACTGATAAATATTATAATTTGGTTTTTACTATTAAGTGTTTGCCTAGGTTCTTTAATCTAC +TCAACCGCTGCTTTAGGTGTTTTAATGTCTAATTTAGGCATGCCTTCTTACTGTACTGGTTACAGAGAAG +GCTATTTGAACTCTACTAATGTCACTATTGCAACCTACTGTACTGGTTCTATACCTTGTAGTGTTTGTCT +TAGTGGTTTAGATTCTTTAGACACCTATCCTTCTTTAGAAACTATACAAATTACCATTTCATCTTTTAAA +TGGGATTTAACTGCTTTTGGCTTAGTTGCAGAGTGGTTTTTGGCATATATTCTTTTCACTAGGTTTTTCT +ATGTACTTGGATTGGCTGCAATCATGCAATTGTTTTTCAGCTATTTTGCAGTACATTTTATTAGTAATTC +TTGGCTTATGTGGTTAATAATTAATCTTGTACAAATGGCCCCGATTTCAGCTATGGTTAGAATGTACATC +TTCTTTGCATCATTTTATTATGTATGGAAAAGTTATGTGCATGTTGTAGACGGTTGTAATTCATCAACTT +GTATGATGTGTTACAAACGTAATAGAGCAACAAGAGTCGAATGTACAACTATTGTTAATGGTGTTAGAAG +GTCCTTTTATGTCTATGCTAATGGAGGTAAAGGCTTTTGCAAACTACACAATTGGAATTGTGTTAATTGT +GATACATTCTGTGCTGGTAGTACATTTATTAGTGATGAAGTTGCGAGAGACTTGTCACTACAGTTTAAAA +GACCAATAAATCCTACTGACCAGTCTTCTTACATCGTTGATAGTGTTACAGTGAAGAATGGTTCCATCCA +TCTTTACTTTGATAAAGCTGGTCAAAAGACTTATGAAAGACATTCTCTCTCTCATTTTGTTAACTTAGAC +AACCTGAGAGCTAATAACACTAAAGGTTCATTGCCTATTAATGTTATAGTTTTTGATGGTAAATCAAAAT +GTGAAGAATCATCTGCAAAATCAGCGTCTGTTTACTACAGTCAGCTTATGTGTCAACCTATACTGTTACT +AGATCAGGCATTAGTGTCTGATGTTGGTGATAGTGCGGAAGTTGCAGTTAAAATGTTTGATGCTTACGTT +AATACGTTTTCATCAACTTTTAACGTACCAATGGAAAAACTCAAAACACTAGTTGCAACTGCAGAAGCTG +AACTTGCAAAGAATGTGTCCTTAGACAATGTCTTATCTACTTTTATTTCAGCAGCTCGGCAAGGGTTTGT +TGATTCAGATGTAGAAACTAAAGATGTTGTTGAATGTCTTAAATTGTCACATCAATCTGACATAGAAGTT +ACTGGCGATAGTTGTAATAACTATATGCTCACCTATAACAAAGTTGAAAACATGACACCCCGTGACCTTG +GTGCTTGTATTGACTGTAGTGCGCGTCATATTAATGCGCAGGTAGCAAAAAGTCACAACATTGCTTTGAT +ATGGAACGTTAAAGATTTCATGTCATTGTCTGAACAACTACGAAAACAAATACGTAGTGCTGCTAAAAAG +AATAACTTACCTTTTAAGTTGACATGTGCAACTACTAGACAAGTTGTTAATGTTGTAACAACAAAGATAG +CACTTAAGGGTGGTAAAATTGTTAATAATTGGTTGAAGCAGTTAATTAAAGTTACACTTGTGTTCCTTTT +TGTTGCTGCTATTTTCTATTTAATAACACCTGTTCATGTCATGTCTAAACATACTGACTTTTCAAGTGAA +ATCATAGGATACAAGGCTATTGATGGTGGTGTCACTCGTGACATAGCATCTACAGATACTTGTTTTGCTA +ACAAACATGCTGATTTTGACACATGGTTTAGCCAGCGTGGTGGTAGTTATACTAATGACAAAGCTTGCCC +ATTGATTGCTGCAGTCATAACAAGAGAAGTGGGTTTTGTCGTGCCTGGTTTGCCTGGCACGATATTACGC +ACAACTAATGGTGACTTTTTGCATTTCTTACCTAGAGTTTTTAGTGCAGTTGGTAACATCTGTTACACAC +CATCAAAACTTATAGAGTACACTGACTTTGCAACATCAGCTTGTGTTTTGGCTGCTGAATGTACAATTTT +TAAAGATGCTTCTGGTAAGCCAGTACCATATTGTTATGATACCAATGTACTAGAAGGTTCTGTTGCTTAT +GAAAGTTTACGCCCTGACACACGTTATGTGCTCATGGATGGCTCTATTATTCAATTTCCTAACACCTACC +TTGAAGGTTCTGTTAGAGTGGTAACAACTTTTGATTCTGAGTACTGTAGGCACGGCACTTGTGAAAGATC +AGAAGCTGGTGTTTGTGTATCTACTAGTGGTAGATGGGTACTTAACAATGATTATTACAGATCTTTACCA +GGAGTTTTCTGTGGTGTAGATGCTGTAAATTTACTTACTAATATGTTTACACCACTAATTCAACCTATTG +GTGCTTTGGACATATCAGCATCTATAGTAGCTGGTGGTATTGTAGCTATCGTAGTAACATGCCTTGCCTA +CTATTTTATGAGGTTTAGAAGAGCTTTTGGTGAATACAGTCATGTAGTTGCCTTTAATACTTTACTATTC +CTTATGTCATTCACTGTACTCTGTTTAACACCAGTTTACTCATTCTTACCTGGTGTTTATTCTGTTATTT +ACTTGTACTTGACATTTTATCTTACTAATGATGTTTCTTTTTTAGCACATATTCAGTGGATGGTTATGTT +CACACCTTTAGTACCTTTCTGGATAACAATTGCTTATATCATTTGTATTTCCACAAAGCATTTCTATTGG +TTCTTTAGTAATTACCTAAAGAGACGTGTAGTCTTTAATGGTGTTTCCTTTAGTACTTTTGAAGAAGCTG +CGCTGTGCACCTTTTTGTTAAATAAAGAAATGTATCTAAAGTTGCGTAGTGATGTGCTATTACCTCTTAC +GCAATATAATAGATACTTAGCTCTTTATAATAAGTACAAGTATTTTAGTGGAGCAATGGATACAACTAGC +TACAGAGAAGCTGCTTGTTGTCATCTCGCAAAGGCTCTCAATGACTTCAGTAACTCAGGTTCTGATGTTC +TTTACCAACCACCACAAACCTCTATCACCTCAGCTGTTTTGCAGAGTGGTTTTAGAAAAATGGCATTCCC +ATCTGGTAAAGTTGAGGGTTGTATGGTACAAGTAACTTGTGGTACAACTACACTTAACGGTCTTTGGCTT +GATGACGTAGTTTACTGTCCAAGACATGTGATCTGCACCTCTGAAGACATGCTTAACCCTAATTATGAAG +ATTTACTCATTCGTAAGTCTAATCATAATTTCTTGGTACAGGCTGGTAATGTTCAACTCAGGGTTATTGG +ACATTCTATGCAAAATTGTGTACTTAAGCTTAAGGTTGATACAGCCAATCCTAAGACACCTAAGTATAAG +TTTGTTCGCATTCAACCAGGACAGACTTTTTCAGTGTTAGCTTGTTACAATGGTTCACCATCTGGTGTTT +ACCAATGTGCTATGAGGCCCAATTTCACTATTAAGGGTTCATTCCTTAATGGTTCATGTGGTAGTGTTGG +TTTTAACATAGATTATGACTGTGTCTCTTTTTGTTACATGCACCATATGGAATTACCAACTGGAGTTCAT +GCTGGCACAGACTTAGAAGGTAACTTTTATGGACCTTTTGTTGACAGGCAAACAGCACAAGCAGCTGGTA +CGGACACAACTATTACAGTTAATGTTTTAGCTTGGTTGTACGCTGCTGTTATAAATGGAGACAGGTGGTT +TCTCAATCGATTTACCACAACTCTTAATGACTTTAACCTTGTGGCTATGAAGTACAATTATGAACCTCTA +ACACAAGACCATGTTGACATACTAGGACCTCTTTCTGCTCAAACTGGAATTGCCGTTTTAGATATGTGTG +CTTCATTAAAAGAATTACTGCAAAATGGTATGAATGGACGTACCATATTGGGTAGTGCTTTATTAGAAGA +TGAATTTACACCTTTTGATGTTGTTAGACAATGCTCAGGTGTTACTTTCCAAAGTGCAGTGAAAAGAACA +ATCAAGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAGTTTTAGTCCAGAGTACTC +AATGGTCTTTGTTCTTTTTTTTGTATGAAAATGCCTTTTTACCTTTTGCTATGGGTATTATTGCTATGTC +TGCTTTTGCAATGATGTTTGTCAAACATAAGCATGCATTTCTCTGTTTGTTTTTGTTACCTTCTCTTGCC +ACTGTAGCTTATTTTAATATGGTCTATATGCCTGCTAGTTGGGTGATGCGTATTATGACATGGTTGGATA +TGGTTGATACTAGTTTGTCTGGTTTTAAGCTAAAAGACTGTGTTATGTATGCATCAGCTGTAGTGTTACT +AATCCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTG +ACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCT +CTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTG +TGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTTTATTGTTTC +TTAGGCTATTTTTGTACTTGTTACTTTGGCCTCTTTTGTTTACTCAACCGCTACTTTAGACTGACTCTTG +GTGTTTATGATTACTTAGTTTCTACACAGGAGTTTAGATATATGAATTCACAGGGACTACTCCCACCCAA +GAATAGCATAGATGCCTTCAAACTCAACATTAAATTGTTGGGTGTTGGTGGCAAACCTTGTATCAAAGTA +GCCACTGTACAGTCTAAAATGTCAGATGTAAAGTGCACATCAGTAGTCTTACTCTCAGTTTTGCAACAAC +TCAGAGTAGAATCATCATCTAAATTGTGGGCTCAATGTGTCCAGTTACACAATGACATTCTCTTAGCTAA +AGATACTACTGAAGCCTTTGAAAAAATGGTTTCACTACTTTCTGTTTTGCTTTCCATGCAGGGTGCTGTA +GACATAAACAAGCTTTGTGAAGAAATGCTGGACAACAGGGCAACCTTACAAGCTATAGCCTCAGAGTTTA +GTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGCTAATGGTGA +TTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCA +GCCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTG +AGGACAAGAGGGCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAA +TGATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACA +ACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAATACGTGTGATGGTACAACAT +TTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTAGATGCAGATAGTAAAATTGTTCAACTTAG +TGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCT +GCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTA +CACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAACACAACAAAGGGAGGTAGGTTTGTACT +TGCACTGTTATCCGATTTACAGGATTTGAAATGGGCTAGATTCCCTAAGAGTGATGGAACTGGTACTATC +TATACAGAACTGGAACCACCTTGTAGGTTTGTTACAGACACACCTAAAGGTCCTAAAGTGAAGTATTTAT +ACTTTATTAAAGGATTAAACAACCTAAATAGAGGTATGGTACTTGGTAGTTTAGCTGCCACAGTACGTCT +ACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGAT +GCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGT +GTACACACACTGGTACTGGTCAGGCAATAACAGTTACACCGGAAGCCAATATGGATCAAGAATCCTTTGG +TGGTGCATCGTGTTGTCTGTACTGCCGTTGCCACATAGATCATCCAAATCCTAAAGGATTTTGTGACTTA +AAAGGTAAGTATGTACAAATACCTACAACTTGTGCTAATGACCCTGTGGGTTTTACACTTAAAAACACAG +TCTGTACCGTCTGCGGTATGTGGAAAGGTTATGGCTGTAGTTGTGATCAACTCCGCGAACCCATGCTTCA +GTCAGCTGATGCACAATCGTTTTTAAACGGGTTTGCGGTGTAAGTGCAGCCCGTCTTACACCGTGCGGCA +CAGGCACTAGTACTGATGTCGTATACAGGGCTTTTGACATCTACAATGATAAAGTAGCTGGTTTTGCTAA +ATTCCTAAAAACTAATTGTTGTCGCTTCCAAGAAAAGGACGAAGATGACAATTTAATTGATTCTTACTTT +GTAGTTAAGAGACACACTTTCTCTAACTACCAACATGAAGAAACAATTTATAATTTACTTAAGGATTGTC +CAGCTGTTGCTAAACATGACTTCTTTAAGTTTAGAATAGACGGTGACATGGTACCACATATATCACGTCA +ACGTCTTACTAAATACACAATGGCAGACCTCGTCTATGCTTTAAGGCATTTTGATGAAGGTAATTGTGAC +ACATTAAAAGAAATACTTGTCACATACAATTGTTGTGATGATGATTATTTCAATAAAAAGGACTGGTATG +ATTTTGTAGAAAACCCAGATATATTACGCGTATACGCCAACTTAGGTGAACGTGTACGCCAAGCTTTGTT +AAAAACAGTACAATTCTGTGATGCCATGCGAAATGCTGGTATTGTTGGTGTACTGACATTAGATAATCAA +GATCTCAATGGTAACTGGTATGATTTCGGTGATTTCATACAAACCACGCCAGGTAGTGGAGTTCCTGTTG +TAGATTCTTATTATTCATTGTTAATGCCTATATTAACCTTGACCAGGGCTTTAACTGCAGAGTCACATGT +TGACACTGACTTAACAAAGCCTTACATTAAGTGGGATTTGTTAAAATATGACTTCACGGAAGAGAGGTTA +AAACTCTTTGACCGTTATTTTAAATATTGGGATCAGACATACCACCCAAATTGTGTTAACTGTTTGGATG +ACAGATGCATTCTGCATTGTGCAAACTTTAATGTTTTATTCTCTACAGTGTTCCCACCTACAAGTTTTGG +ACCACTAGTGAGAAAAATATTTGTTGATGGTGTTCCATTTGTAGTTTCAACTGGATACCACTTCAGAGAG +CTAGGTGTTGTACATAATCAGGATGTAAACTTACATAGCTCTAGACTTAGTTTTAAGGAATTACTTGTGT +ATGCTGCTGACCCTGCTATGCACGCTGCTTCTGGTAATCTATTACTAGATAAACGCACTACGTGCTTTTC +AGTAGCTGCACTTACTAACAATGTTGCTTTTCAAACTGTCAAACCCGGTAATTTTAACAAAGACTTCTAT +GACTTTGCTGTGTCTAAGGGTTTCTTTAAGGAAGGAAGTTCTGTTGAATTAAAACACTTCTTCTTTGCTC +AGGATGGTAATGCTGCTATCAGCGATTATGACTACTATCGTTATAATCTACCAACAATGTGTGATATCAG +ACAACTACTATTTGTAGTTGAAGTTGTTGATAAGTACTTTGATTGTTACGATGGTGGCTGTATTAATGCT +AACCAAGTCATCGTCAACAACCTAGACAAATCAGCTGGTTTTCCATTTAATAAATGGGGTAAGGCTAGAC +TTTATTATGATTCAATGAGTTATGAGGATCAAGATGCACTTTTCGCATATACAAAACGTAATGTCATCCC +TACTATAACTCAAATGAATCTTAAGTATGCCATTAGTGCAAAGAATAGAGCTCGCACCGTAGCTGGTGTC +TCTATCTGTAGTACTATGACCAATAGACAGTTTCATCAAAAATTATTGAAATCAATAGCCGCCACTAGAG +GAGCTACTGTAGTAATTGGAACAAGCAAATTCTATGGTGGTTGGCACAACATGTTAAAAACTGTTTATAG +TGATGTAGAAAACCCTCACCTTATGGGTTGGGATTATCCTAAATGTGATAGAGCCATGCCTAACATGCTT +AGAATTATGGCCTCACTTGTTCTTGCTCGCAAACATACAACGTGTTGTAGCTTGTCACACCGTTTCTATA +GATTAGCTAATGAGTGTGCTCAAGTATTGAGTGAAATGGTCATGTGTGGCGGTTCACTATATGTTAAACC +AGGTGGAACCTCATCAGGAGATGCCACAACTGCTTATGCTAATAGTGTTTTTAACATTTGTCAAGCTGTC +ACGGCCAATGTTAATGCACTTTTATCTACTGATGGTAACAAAATTGCCGATAAGTATGTCCGCAATTTAC +AACACAGACTTTATGAGTGTCTCTATAGAAATAGAGATGTTGACACAGACTTTGTGAATGAGTTTTACGC +ATATTTGCGTAAACATTTCTCAATGATGATACTCTCTGACGATGCTGTTGTGTGTTTCAATAGCACTTAT +GCATCTCAAGGTCTAGTGGCTAGCATAAAGAACTTTAAGTCAGTTCTTTATTATCAAAACAATGTTTTTA +TGTCTGAAGCAAAATGTTGGACTGAGACTGACCTTACTAAAGGACCTCATGAATTTTGCTCTCAACATAC +AATGCTAGTTAAACAGGGTGATGATTATGTGTACCTTCCTTACCCAGATCCATCAAGAATCCTAGGGGCC +GGCTGTTTTGTAGATGATATCGTAAAAACAGATGGTACACTTATGATTGAACGGTTCGTGTCTTTAGCTA +TAGATGCTTACCCACTTACTAAACATCCTAATCAGGAGTATGCTGATGTCTTTCATTTGTACTTACAATA +CATAAGAAAGCTACATGATGAGTTAACAGGACACATGTTAGACATGTATTCTGTTATGCTTACTAATGAT +AACACTTCAAGGTATTGGGAACCTGAGTTTTATGAGGCTATGTACACACCGCATACAGTCTTACAGGCTG +TTGGGGCTTGTGTTCTTTGCAATTCACAGACTTCATTAAGATGTGGTGCTTGCATACGTAGACCATTCTT +ATGTTGTAAATGCTGTTACGACCATGTCATATCAACATCACATAAATTAGTCTTGTCTGTTAATCCGTAT +GTTTGCAATGCTCCAGGTTGTGATGTCACAGATGTGACTCAACTTTACTTAGGAGGTATGAGCTATTATT +GTAAATCACATAAACCACCCATTAGTTTTCCATTGTGTGCTAATGGACAAGTTTTTGGTTTATATAAAAA +TACATGTGTTGGTAGCGATAATGTTACTGACTTTAATGCAATTGCAACATGTGACTGGACAAATGCTGGT +GATTACATTTTAGCTAACACCTGTACTGAAAGACTCAAGCTTTTTGCAGCAGAAACGCTCAAAGCTACTG +AGGAGACATTTAAACTGTCTTATGGTATTGCTACTGTACGTGAAGTGCTGTCTGACAGAGAATTACATCT +TTCATGGGAAGTTGGTAAACCTAGACCACCACTTAACCGAAATTATGTCTTTACTGGTTATCGTGTAACT +AAAAACAGTAAAGTACAAATAGGAGAGTACACCTTTGAAAAAGGTGACTATGGTGATGCTGTTGTTTACC +GAGGTACAACAACTTACAAATTAAATGTTGGTGATTATTTTGTGCTGACATCACATACAGTAATGCCATT +AAGTGCACCTACACTAGTGCCACAAGAGCACTATGTTAGAATTACTGGCTTATACCCAACACTCAATATC +TCAGATGAGTTTTCTAGCAATGTTGCAAATTATCAAAAGGTTGGTATGCAAAAGTATTCTACACTCCAGG +GACCACCTGGTACTGGTAAGAGTCATTTTGCTATTGGCCTAGCTCTCTACTACCCTTCTGCTCGCATAGT +GTATACAGCTTGCTCTCATGCCGCTGTTGATGCACTATGTGAGAAGGCATTAAAATATTTGCCTATAGAT +AAATGTAGTAGAATTATACCTGCACGTGCTCGTGTAGAGTGTTTTGATAAATTCAAAGTGAATTCAACAT +TAGAACAGTATGTCTTTTGTACTGTAAATGCATTGCCTGAGACGACAGCAGATATAGTTGTCTTTGATGA +AATTTCAATGGCCACAAATTATGATTTGAGTGTTGTCAATGCCAGATTACGTGCTAAGCACTATGTGTAC +ATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATT +TCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCC +TGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGATAATAAGCTTAAAGCACATAAAGACAAATCA +GCTCAATGCTTTAAAATGTTTTATAAGGGTGTTATCACGCATGATGTTTCATCTGCAATTAACAGGCCAC +AAATAGGCGTGGTAAGAGAATTCCTTACACGTAACCCTGCTTGGAGAAAAGCTGTCTTTATTTCACCTTA +TAATTCACAGAATGCTGTAGCCTCAAAGATTTTGGGACTACCAACTCAAACTGTTGATTCATCACAGGGC +TCAGAATATGACTATGTCATATTCACTCAAACCACTGAAACAGCTCACTCTTGTAATGTAAACAGATTTA +ATGTTGCTATTACCAGAGCAAAAGTAGGCATACTTTGCATAATGTCTGATAGAGACCTTTATGACAAGTT +GCAATTTACAAGTCTTGAAATTCCACGTAGGAATGTGGCAACTTTACAAGCTGAAAATGTAACAGGACTC +TTTAAAGATTGTAGTAAGGTAATCACTGGGTTACATCCTACACAGGCACCTACACACCTCAGTGTTGACA +CTAAATTCAAAACTGAAGGTTTATGTGTTGACATACCTGGCATACCTAAGGACATGACCTATAGAAGACT +CATCTCTATGATGGGTTTTAAAATGAATTATCAAGTTAATGGTTACCCTAACATGTTTATCACCCGCGAA +GAAGCTATAAGACATGTACGTGCATGGATTGGCTTCGATGTCGAGGGGTGTCATGCTACTAGAGAAGCTG +TTGGTACCAATTTACCTTTACAGCTAGGTTTTTCTACAGGTGTTAACCTAGTTGCTGTACCTACAGGTTA +TGTTGATACACCTAATAATACAGATTTTTCCAGAGTTAGTGCTAAACCACCGCCTGGAGATCAATTTAAA +CACCTCATACCACTTATGTACAAAGGACTTCCTTGGAATGTAGTGCGTATAAAGATTGTACAAATGTTAA +GTGACACACTTAAAAATCTCTCTGACAGAGTCGTATTTGTCTTATGGGCACATGGCTTTGAGTTGACATC +TATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTT +TCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTA +TGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCA +TGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTT +AAGCGTGTTGACTGGACTATTGAATATCCTATAATTGGTGATGAACTGAAGATTAATGCGGCTTGTAGAA +AGGTTCAACACATGGTTGTTAAAGCTGCATTATTAGCAGACAAATTCCCAGTTCTTCACGACATTGGTAA +CCCTAAAGCTATTAAGTGTGTACCTCAAGCTGATGTAGAATGGAAGTTCTATGATGCACAGCCTTGTAGT +GACAAAGCTTATAAAATAGAAGAATTATTCTATTCTTATGCCACACATTCTGACAAATTCACAGATGGTG +TATGCCTATTTTGGAATTGCAATGTCGATAGATATCCTGCTAATTCCATTGTTTGTAGATTTGACACTAG +AGTGCTATCTAACCTTAACTTGCCTGGTTGTGATGGTGGCAGTTTGTATGTAAATAAACATGCATTCCAC +ACACCAGCTTTTGATAAAAGTGCTTTTGTTAATTTAAAACAATTACCATTTTTCTATTACTCTGACAGTC +CATGTGAGTCTCATGGAAAACAAGTAGTGTCAGATATAGATTATGTACCACTAAAGTCTGCTACGTGTAT +AACACGTTGCAATTTAGGTGGTGCTGTCTGTAGACATCATGCTAATGAGTACAGATTGTATCTCGATGCT +TATAACATGATGATCTCAGCTGGCTTTAGCTTGTGGGTTTACAAACAATTTGATACTTATAACCTCTGGA +ACACTTTTACAAGACTTCAGAGTTTAGAAAATGTGGCTTTTAATGTTGTAAATAAGGGACACTTTGATGG +ACAACAGGGTGAAGTACCAGTTTCTATCATTAATAACACTGTTTACACAAAAGTTGATGGTGTTGATGTA +GAATTGTTTGAAAATAAAACAACATTACCTGTTAATGTAGCATTTGAGCTTTGGGCTAAGCGCAACATTA +AACCAGTACCAGAGGTGAAAATACTCAATAATTTGGGTGTGGACATTGCTGCTAATACTGTGATCTGGGA +CTACAAAAGAGATGCTCCAGCACATATATCTACTATTGGTGTTTGTTCTATGACTGACATAGCCAAGAAA +CCAACTGAAACGATTTGTGCACCACTCACTGTCTTTTTTGATGGTAGAGTTGATGGTCAAGTAGACTTAT +TTAGAAATGCCCGTAATGGTGTTCTTATTACAGAAGGTAGTGTTAAAGGTTTACAACCATCTGTAGGTCC +CAAACAAGCTAGTCTTAATGGAGTCACATTAATTGGAGAAGCCGTAAAAACACAGTTCAATTATTATAAG +AAAGTTGATGGTGTTGTCCAACAATTACCTGAAACTTACTTTACTCAGAGTAGAAATTTACAAGAATTTA +AACCCAGGAGTCAAATGGAAATTGATTTCTTAGAATTAGCTATGGATGAATTCATTGAACGGTATAAATT +AGAAGGCTATGCCTTCGAACATATCGTTTATGGAGATTTTAGTCATAGTCAGTTAGGTGGTTTACATCTA +CTGATTGGACTAGCTAAACGTTTTAAGGAATCACCTTTTGAATTAGAAGATTTTATTCCTATGGACAGTA +CAGTTAAAAACTATTTCATAACAGATGCGCAAACAGGTTCATCTAAGTGTGTGTGTTCTGTTATTGATTT +ATTACTTGATGATTTTGTTGAAATAATAAAATCCCAAGATTTATCTGTAGTTTCTAAGGTTGTCAAAGTG +ACTATTGACTATACAGAAATTTCATTTATGCTTTGGTGTAAAGATGGCCATGTAGAAACATTTTACCCAA +AATTACAATCTAGTCAAGCGTGGCAACCGGGTGTTGCTATGCCTAATCTTTACAAAATGCAAAGAATGCT +ATTAGAAAAGTGTGACCTTCAAAATTATGGTGATAGTGCAACATTACCTAAAGGCATAATGATGAATGTC +GCAAAATATACTCAACTGTGTCAATATTTAAACACATTAACATTAGCTGTACCCTATAATATGAGAGTTA +TACATTTTGGTGCTGGTTCTGATAAAGGAGTTGCACCAGGTACAGCTGTTTTAAGACAGTGGTTGCCTAC +GGGTACGCTGCTTGTCGATTCAGATCTTAATGACTTTGTCTCTGATGCAGATTCAACTTTGATTGGTGAT +TGTGCAACTGTACATACAGCTAATAAATGGGATCTCATTATTAGTGATATGTACGACCCTAAGACTAAAA +ATGTTACAAAAGAAAATGACTCTAAAGAGGGTTTTTTCACTTACATTTGTGGGTTTATACAACAAAAGCT +AGCTCTTGGAGGTTCCGTGGCTATAAAGATAACAGAACATTCTTGGAATGCTGATCTTTATAAGCTCATG +GGACACTTCGCATGGTGGACAGCCTTTGTTACTAATGTGAATGCGTCATCATCTGAAGCATTTTTAATTG +GATGTAATTATCTTGGCAAACCACGCGAACAAATAGATGGTTATGTCATGCATGCAAATTACATATTTTG +GAGGAATACAAATCCAATTCAGTTGTCTTCCTATTCTTTATTTGACATGAGTAAATTTCCCCTTAAATTA +AGGGGTACTGCTGTTATGTCTTTAAAAGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAG +GTAGACTTATAATTAGAGAAAACAACAGAGTTGTTATTTCTAGTGATGTTCTTGTTAACAACTAAACGAA +CAATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCA +ATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCA +GTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATG +TCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGC +TTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCC +CTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCAT +TTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGC +GAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTC +AAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTA +TTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTAT +TAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCA +GGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATA +ATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTT +GAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATT +GTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTG +TTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATC +ATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTAT +GCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTG +ATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTC +TAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGA +GATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACT +TTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACT +TTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAAC +AAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTC +TGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGA +GATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAAC +CAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTA +CTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGC +TGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACT +CAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTG +GTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTAC +CACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCA +ACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAA +TAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACC +AATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCA +TTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATT +GCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACC +TTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGG +ACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTG +GAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAA +AATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCA +CAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATA +TCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAG +TTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCT +ACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTA +TGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAA +GAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTT +TCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACA +CATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACC +TGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTA +GGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTG +CCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCC +ATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGT +ATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACG +ACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACATAAACGAACTTATGGATTTGTTTATGAGA +ATCTTCACAATTGGAACTGTAACTTTGAAGCAAGGTGAAATCAAGGATGCTACTCCTTCAGATTTTGTTC +GCGCTACTGCAACGATACCGATACAAGCCTCACTCCCTTTCGGATGGCTTATTGTTGGCGTTGCACTTCT +TGCTGTTTTTCAGAGCGCTTCCAAAATCATAACCCTCAAAAAGAGATGGCAACTAGCACTCTCCAAGGGT +GTTCACTTTGTTTGCAACTTGCTGTTGTTGTTTGTAACAGTTTACTCACACCTTTTGCTCGTTGCTGCTG +GCCTTGAAGCCCCTTTTCTCTATCTTTATGCTTTAGTCTACTTCTTGCAGAGTATAAACTTTGTAAGAAT +AATAATGAGGCTTTGGCTTTGCTGGAAATGCCGTTCCAAAAACCCATTACTTTATGATGCCAACTATTTT +CTTTGCTGGCATACTAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTA +CTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATG +GGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCA +ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGC +CTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAAT +TTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTAC +TCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT +TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGT +GAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT +CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGA +TTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTC +CTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTA +AGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAAT +AAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTC +ATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC +TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGT +GATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAA +GAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTG +ACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAG +CAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC +TATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA +AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAAC +CAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGA +GCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACA +TACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAAT +TTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACT +GTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT +ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTG +CTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAA +GATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTG +TAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCC +GTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAA +TTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT +GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGA +AGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTG +ATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAG +TAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACT +GCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTC +CAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG +TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCT +GGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAA +AAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAAC +ATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGT +AGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCA +ATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG +TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGG +CAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCC +AAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACA +ATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACG +TGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGC +TGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC +TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGAT +TTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATG +CAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTT +GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT +TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC +GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT +TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAA -- cgit v1.2.3 From ffad8c21f08aca1cf65809c398f3613846e7c8ba Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Fri, 10 Apr 2020 16:47:31 -0400 Subject: Propagating metadata to output works now. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- bh20seqanalyzer/main.py | 4 ++-- bh20sequploader/bh20seq-schema.yml | 5 ----- bh20sequploader/qc_metadata.py | 26 +------------------------- example/metadata.yaml | 2 -- 4 files changed, 3 insertions(+), 34 deletions(-) (limited to 'bh20sequploader') diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 63ff067..193a268 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -29,7 +29,7 @@ def validate_upload(api, collection, validated_project, else: try: metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml")) - metadata_content["id"] = "keep:%s/metadata.yaml" % collection["portable_data_hash"] + metadata_content["id"] = "http://arvados.org/keep:%s/metadata.yaml" % collection["portable_data_hash"] add_lc_filename(metadata_content, metadata_content["id"]) valid = qc_metadata(metadata_content) and valid except Exception as e: @@ -146,7 +146,7 @@ def start_pangenome_analysis(api, "class": "File", "location": "keep:%s/metadata.yaml" % v["portable_data_hash"] }) - inputobj["subjects"].append("keep:%s/sequence.fasta" % v["portable_data_hash"]) + inputobj["subjects"].append("http://arvados.org/keep:%s/sequence.fasta" % v["portable_data_hash"]) run_workflow(api, analysis_project, pangenome_workflow_uuid, "Pangenome analysis", inputobj) diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index a072bd7..8a22db1 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -169,11 +169,6 @@ $graph: virus: virusSchema? technology: technologySchema submitter: submitterSchema - submission: - type: string - jsonldPredicate: - _id: "@id" - #_type: "@id" id: doc: The subject (eg the fasta/fastq file) that the metadata describes type: string? diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py index 38edcaa..e477f21 100644 --- a/bh20sequploader/qc_metadata.py +++ b/bh20sequploader/qc_metadata.py @@ -5,21 +5,10 @@ import pkg_resources import logging import traceback -class CustomFetcher(schema_salad.ref_resolver.DefaultFetcher): - def check_exists(sup, url): - if url.startswith("keep:"): - return True - else: - return super().check_exists(url) - - def supported_schemes(self): # type: () -> List[str] - return ["file", "http", "https", "mailto", "keep"] - - def qc_metadata(metadatafile): schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml") cache = {"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml": schema_resource.read().decode("utf-8")} - (loader, + (document_loader, avsc_names, schema_metadata, metaschema_loader) = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache) @@ -28,19 +17,6 @@ def qc_metadata(metadatafile): print(avsc_names) return False - document_loader = schema_salad.ref_resolver.Loader( - loader.ctx, - schemagraph=loader.graph, - foreign_properties=loader.foreign_properties, - idx=loader.idx, - cache=loader.cache, - fetcher_constructor=CustomFetcher, - skip_schemas=loader.skip_schemas, - url_fields=loader.url_fields, - allow_attachments=loader.allow_attachments, - session=loader.session, - ) - try: doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True) return True diff --git a/example/metadata.yaml b/example/metadata.yaml index a2f6e57..c780921 100644 --- a/example/metadata.yaml +++ b/example/metadata.yaml @@ -1,5 +1,3 @@ -submission: publicSequenceResource - host: host_id: XX1 host_species: string -- cgit v1.2.3 From 4f4229a61e63649730e7120c764f364078860f0f Mon Sep 17 00:00:00 2001 From: lltommy Date: Sat, 11 Apr 2020 02:44:04 +0200 Subject: Adding descriptions to the yml schema, slight changes to the yml schema --- bh20sequploader/bh20seq-schema.yml | 45 ++++++++++++++++++++++++++++++++------ example/metadata.yaml | 5 +++-- example/minimal_example.yaml | 6 ++--- 3 files changed, 44 insertions(+), 12 deletions(-) (limited to 'bh20sequploader') diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 8a22db1..c259f16 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -13,41 +13,51 @@ $graph: type: record fields: host_species: + doc: Host species as defined in NCBITaxon (e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 for Homo sapiens) type: string jsonldPredicate: _id: http://www.ebi.ac.uk/efo/EFO_0000532 host_id: + doc: Identifer for the host. If you submit multiple samples from the same host, use the same host_id for those samples type: string jsonldPredicate: _id: http://semanticscience.org/resource/SIO_000115 host_common_name: + doc: Text label for the host species (e.g. homo sapiens) type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/NOMEN_0000037 host_sex: + doc: Sex of the host as define in NCIT, IRI expected (http://purl.obolibrary.org/obo/C20197 (Male), http://purl.obolibrary.org/obo/NCIT_C27993 (Female) or unkown (http://purl.obolibrary.org/obo/NCIT_C17998)) type: string jsonldPredicate: _id: http://purl.obolibrary.org/obo/PATO_0000047 host_age: + doc: Age of the host as number (e.g. 50) type: int? jsonldPredicate: _id: http://purl.obolibrary.org/obo/PATO_0000011 host_age_unit: + doc: Unit of host age.... this field is unstable as of now (might be removed) type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/UO_0000036 host_health_status: + doc: A condition or state at a particular time type: string? jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688 host_treatment: + doc: Process in which the act is intended to modify or alter type: string? jsonldPredicate: _id: http://www.ebi.ac.uk/efo/EFO_0000727 host_vaccination: + doc: Field is unstable type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/VO_0000001 additional_host_information: + doc: Field for additional host information type: string? jsonldPredicate: _id: http://semanticscience.org/resource/SIO_001167 @@ -56,38 +66,47 @@ $graph: type: record fields: collector_name: + doc: Name of the person that took the sample type: string jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0001895 collecting_institution: + doc: Institute that was responsible of sampeling type: string jsonldPredicate: _id: http://semanticscience.org/resource/SIO_001167 specimen_source: + doc: A specimen that derives from an anatomical part or substance arising from an organism, e.g. tissue, organ type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0001479 collection_date: + doc: Date when the sample was taken type: string? jsonldPredicate: _id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164 collection_location: + doc: Geographical location where the sample was collected as Gazetteer (https://www.ebi.ac.uk/ols/ontologies/gaz) reference, e.g. http://purl.obolibrary.org/obo/GAZ_00002845 (China) type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/GAZ_00000448 sample_storage_conditions: + doc: Information aboout storage of a specified type, e.g. frozen specimen, paraffin, fresh .... type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0001472 additional_collection_information: + doc: Add additional comment about the circumstances that a sample was taken type: string? jsonldPredicate: _id: http://semanticscience.org/resource/SIO_001167 sample_id: + doc: Id of the sample as defined by the submitter type: string jsonldPredicate: _id: http://semanticscience.org/resource/SIO_000115 source_database_accession: + doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here type: string? jsonldPredicate: _id: http://edamontology.org/data_2091 @@ -96,10 +115,12 @@ $graph: type: record fields: virus_species: + doc: The name of a taxon from the NCBI taxonomy database type: string? jsonldPredicate: _id: http://edamontology.org/data_1875 virus_strain: + doc: Name of the virus strain type: string? jsonldPredicate: _id: http://semanticscience.org/resource/SIO_010055 @@ -108,14 +129,17 @@ $graph: type: record fields: sample_sequencing_technology: + doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION) type: string jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0600047 sequence_assembly_method: + doc: Protocol which provides instructions on the alignment of sequencing reads to reference genome type: string? jsonldPredicate: _id: http://www.ebi.ac.uk/efo/EFO_0002699 sequencing_coverage: + doc: Sequence coverage defined as the average number of reads representing a given nucleotide (e.g. 100x) type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/FLU_0000848 @@ -124,22 +148,22 @@ $graph: type: record fields: submitter_name: + doc: Name of the submitter type: string jsonldPredicate: _id: http://semanticscience.org/resource/SIO_000116 - submitter_date: - type: string - jsonldPredicate: - _id: http://purl.obolibrary.org/obo/NCIT_C94162 submitter_address: + doc: Address of the submitter type: string? jsonldPredicate: _id: http://semanticscience.org/resource/SIO_000172 originating_lab: + doc: Name of the laboratory that took the sample type: string jsonldPredicate: _id: http://purl.obolibrary.org/obo/NCIT_C37984 lab_address: + doc: Address of the laboratory where the sample was taken type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0600047 @@ -152,10 +176,17 @@ $graph: jsonldPredicate: _id: http://www.ebi.ac.uk/efo/EFO_0001741 authors: + doc: Name of the author(s) type: string? jsonldPredicate: _id: http://purl.obolibrary.org/obo/NCIT_C42781 - submitter_id: + publication: + doc: Reference to publication of this sample (e.g. DOI, pubmed ID, ...) + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C19026 + submitter_orchid: + doc: ORCHID of the submitter type: string? jsonldPredicate: _id: http://semanticscience.org/resource/SIO_000115 @@ -171,7 +202,7 @@ $graph: submitter: submitterSchema id: doc: The subject (eg the fasta/fastq file) that the metadata describes - type: string? + type: string jsonldPredicate: _id: "@id" - _type: "@id" + #_type: "@id" # Error (contains undefined reference) if I keep this file but we need a toplevel id to tie things together diff --git a/example/metadata.yaml b/example/metadata.yaml index c780921..d9e8e92 100644 --- a/example/metadata.yaml +++ b/example/metadata.yaml @@ -1,3 +1,5 @@ +id: placeholder + host: host_id: XX1 host_species: string @@ -36,5 +38,4 @@ submitter: provider_sample_id: string submitter_sample_id: string authors: testAuthor - submitter_id: X12 - submitter_date: Subdate + submitter_orchid: X12 diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml index f312ab7..160d1d4 100644 --- a/example/minimal_example.yaml +++ b/example/minimal_example.yaml @@ -1,8 +1,9 @@ -submission: publicSequenceResource +id: placeholder host: host_id: XX host_species: string + host_sex: string sample: sample_id: XXX @@ -14,5 +15,4 @@ technology: submitter: submitter_name: tester - originating_lab: testLab - submitter_date: Subdate \ No newline at end of file + originating_lab: testLab \ No newline at end of file -- cgit v1.2.3 From 31686ba2e1b2edec29229ab5adb28b366893f17b Mon Sep 17 00:00:00 2001 From: lltommy Date: Sat, 11 Apr 2020 04:02:55 +0200 Subject: Adding noLinkCheck to root --- bh20sequploader/bh20seq-schema.yml | 4 +++- bh20sequploader/rdf-mappings.ttl | 0 2 files changed, 3 insertions(+), 1 deletion(-) create mode 100644 bh20sequploader/rdf-mappings.ttl (limited to 'bh20sequploader') diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index c259f16..81a7f22 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -13,6 +13,7 @@ $graph: type: record fields: host_species: + ## autocomplete # NCBITAXON doc: Host species as defined in NCBITaxon (e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 for Homo sapiens) type: string jsonldPredicate: @@ -205,4 +206,5 @@ $graph: type: string jsonldPredicate: _id: "@id" - #_type: "@id" # Error (contains undefined reference) if I keep this file but we need a toplevel id to tie things together + _type: "@id" + noLinkCheck: true diff --git a/bh20sequploader/rdf-mappings.ttl b/bh20sequploader/rdf-mappings.ttl new file mode 100644 index 0000000..e69de29 -- cgit v1.2.3