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-rw-r--r--bh20sequploader/bh20seq-schema.yml210
-rw-r--r--bh20sequploader/main.py26
-rw-r--r--bh20sequploader/qc_fasta.py28
-rw-r--r--bh20sequploader/qc_metadata.py26
-rw-r--r--bh20sequploader/rdf-mappings.ttl0
-rw-r--r--bh20sequploader/validation/Makefile4
-rw-r--r--bh20sequploader/validation/formats4
-rw-r--r--bh20sequploader/validation/formats.mgcbin0 -> 1032 bytes
8 files changed, 292 insertions, 6 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
new file mode 100644
index 0000000..81a7f22
--- /dev/null
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -0,0 +1,210 @@
+$base: http://biohackathon.org/bh20-seq-schema
+$namespaces:
+ sch: https://schema.org/
+ efo: http://www.ebi.ac.uk/efo/
+ obo: http://purl.obolibrary.org/obo/
+ sio: http://semanticscience.org/resource/
+ edam: http://edamontology.org/
+ evs: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#
+
+$graph:
+
+- name: hostSchema
+ 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:
+ _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
+
+- name: sampleSchema
+ 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
+
+- name: virusSchema
+ 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
+
+- name: technologySchema
+ 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
+
+- name: submitterSchema
+ type: record
+ fields:
+ submitter_name:
+ doc: Name of the submitter
+ type: string
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_000116
+ 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
+ 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:
+ doc: Name of the author(s)
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/NCIT_C42781
+ 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
+
+- name: MainSchema
+ type: record
+ documentRoot: true
+ fields:
+ host: hostSchema
+ sample: sampleSchema
+ virus: virusSchema?
+ technology: technologySchema
+ submitter: submitterSchema
+ id:
+ doc: The subject (eg the fasta/fastq file) that the metadata describes
+ type: string
+ jsonldPredicate:
+ _id: "@id"
+ _type: "@id"
+ noLinkCheck: true
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 17ad492..4a225f6 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -3,9 +3,13 @@ import time
import arvados
import arvados.collection
import json
+import magic
+from pathlib import Path
import urllib.request
import socket
import getpass
+from .qc_metadata import qc_metadata
+from .qc_fasta import qc_fasta
ARVADOS_API_HOST='lugli.arvadosapi.com'
ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
@@ -13,29 +17,36 @@ 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()
api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
+ 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)
- print("Reading FASTA")
- with col.open("sequence.fasta", "w") as f:
+ with col.open(target, "w") as f:
r = args.sequence.read(65536)
print(r[0:20])
while r:
f.write(r)
r = args.sequence.read(65536)
+ args.sequence.close()
- 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:
f.write(r)
r = args.metadata.read(65536)
+ args.metadata.close()
external_ip = urllib.request.urlopen('https://ident.me').read().decode('utf8')
@@ -49,4 +60,7 @@ def main():
(properties['upload_user'], properties['upload_ip']),
properties=properties, ensure_unique_name=True)
-main()
+ print("Done")
+
+if __name__ == "__main__":
+ main()
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
new file mode 100644
index 0000000..e47d66b
--- /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 "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/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
new file mode 100644
index 0000000..e477f21
--- /dev/null
+++ b/bh20sequploader/qc_metadata.py
@@ -0,0 +1,26 @@
+import schema_salad.schema
+import schema_salad.ref_resolver
+import logging
+import pkg_resources
+import logging
+import traceback
+
+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,
+ 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)
+
+ 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 Exception as e:
+ traceback.print_exc()
+ logging.warn(e)
+ return False
diff --git a/bh20sequploader/rdf-mappings.ttl b/bh20sequploader/rdf-mappings.ttl
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/bh20sequploader/rdf-mappings.ttl
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
--- /dev/null
+++ b/bh20sequploader/validation/formats.mgc
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generated by cgit v1.2.3 (git 2.45.0) at 2024-07-06 01:20:58 +0000