diff --git a/ingest/README.md b/ingest/README.md index f2dcdbc1..99084906 100644 --- a/ingest/README.md +++ b/ingest/README.md @@ -84,7 +84,7 @@ These are optional environment variables used in our automated pipeline for prov ### GenBank data GenBank sequences and metadata are fetched via NCBI Virus. -The exact URL used to fetch data is constructed in `bin/genbank-url`. +The exact URL used to fetch data is constructed by `vendored/ncbi-virus-url`. ## `ingest/vendored` diff --git a/ingest/bin/fetch-from-genbank b/ingest/bin/fetch-from-genbank deleted file mode 100755 index 2ecb6768..00000000 --- a/ingest/bin/fetch-from-genbank +++ /dev/null @@ -1,22 +0,0 @@ -#!/bin/bash -# -# Originally copied from "bin/fetch-from-genbank" in nextstrain/ncov-ingest: -# https://github.com/nextstrain/ncov-ingest/blob/2a5f255329ee5bdf0cabc8b8827a700c92becbe4/bin/fetch-from-genbank -# -set -euo pipefail - -bin="$(dirname "$0")" - - -main() { - local ncbi_taxon_id="${1:?NCBI taxon id is required.}" - fetch "$ncbi_taxon_id" | "$bin"/csv-to-ndjson -} - -fetch() { - curl "$("$bin"/genbank-url --ncbi-taxon-id "$1")" \ - --fail --silent --show-error --http1.1 \ - --header 'User-Agent: https://github.com/nextstrain/monkeypox (hello@nextstrain.org)' -} - -main "$@" diff --git a/ingest/vendored/.cramrc b/ingest/vendored/.cramrc new file mode 100644 index 00000000..153d20f5 --- /dev/null +++ b/ingest/vendored/.cramrc @@ -0,0 +1,3 @@ +[cram] +shell = /bin/bash +indent = 2 diff --git a/ingest/vendored/.github/workflows/ci.yaml b/ingest/vendored/.github/workflows/ci.yaml index dcb3b898..bbf40f72 100644 --- a/ingest/vendored/.github/workflows/ci.yaml +++ b/ingest/vendored/.github/workflows/ci.yaml @@ -11,3 +11,11 @@ jobs: steps: - uses: actions/checkout@v3 - uses: nextstrain/.github/actions/shellcheck@master + + cram: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + - run: pip install cram + - run: cram tests/ diff --git a/ingest/vendored/.gitrepo b/ingest/vendored/.gitrepo index 9802a7cc..2aade9fd 100644 --- a/ingest/vendored/.gitrepo +++ b/ingest/vendored/.gitrepo @@ -6,7 +6,7 @@ [subrepo] remote = https://github.com/nextstrain/ingest branch = main - commit = 1eb8b30428d5f66adac201f0a246a7ab4bdc9792 - parent = a7ccb51fecede6336ef06ec2a980db27aa5821b4 + commit = c97df238518171c2b1574bec0349a55855d1e7a7 + parent = fb8175010a16294954d4d4a499edc137bede8265 method = merge cmdver = 0.4.6 diff --git a/ingest/vendored/README.md b/ingest/vendored/README.md index 0311a551..533b39ad 100644 --- a/ingest/vendored/README.md +++ b/ingest/vendored/README.md @@ -69,6 +69,14 @@ Scripts for supporting ingest workflow automation that don’t really belong in - [trigger-on-new-data](trigger-on-new-data) - Triggers downstream GitHub Actions if the provided `upload-to-s3` outputs do not contain the `identical_file_message` A hacky way to ensure that we only trigger downstream phylogenetic builds if the S3 objects have been updated. +NCBI interaction scripts that are useful for fetching public metadata and sequences. + +- [fetch-from-ncbi-entrez](fetch-from-ncbi-entrez) - Fetch metadata and nucleotide sequences from [NCBI Entrez](https://www.ncbi.nlm.nih.gov/books/NBK25501/) and output to a GenBank file. + Useful for pathogens with metadata and annotations in custom fields that are not part of the standard [NCBI Virus](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/) or [NCBI Datasets](https://www.ncbi.nlm.nih.gov/datasets/) outputs. +- [fetch-from-ncbi-virus](fetch-from-ncbi-virus) - Fetch metadata and nucleotide sequences from [NCBI Virus](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/) and output NDJSON records to stdout. +- [ncbi-virus-url](ncbi-virus-url) - Generates the URL to download metadata and sequences from NCBI Virus as a single CSV file. +- [csv-to-ndjson](csv-to-ndjson) - Converts CSV file to NDJSON file with a hard-coded 200MiB field size limit to accommodate sequences in the NCBI Virus download. + Potential Nextstrain CLI scripts - [sha256sum](sha256sum) - Used to check if files are identical in upload-to-s3 and download-from-s3 scripts. @@ -89,3 +97,16 @@ Potential augur curate scripts - [transform-authors](transform-authors) - Abbreviates full author lists to ' et al.' - [transform-field-names](transform-field-names) - Rename fields of NDJSON records - [transform-genbank-location](transform-genbank-location) - Parses `location` field with the expected pattern `"[:][, ]"` based on [GenBank's country field](https://www.ncbi.nlm.nih.gov/genbank/collab/country/) + +## Software requirements + +Some scripts may require Bash ≥4. If you are running these scripts on macOS, the builtin Bash (`/bin/bash`) does not meet this requirement. You can install [Homebrew's Bash](https://formulae.brew.sh/formula/bash) which is more up to date. + +## Testing + +Most scripts are untested within this repo, relying on "testing in production". That is the only practical testing option for some scripts such as the ones interacting with S3 and Slack. + +For more locally testable scripts, Cram-style functional tests live in `tests` and are run as part of CI. To run these locally, + +1. Download Cram: `pip install cram` +2. Run the tests: `cram tests/` diff --git a/ingest/vendored/cloudfront-invalidate b/ingest/vendored/cloudfront-invalidate index dec48529..dbea3981 100755 --- a/ingest/vendored/cloudfront-invalidate +++ b/ingest/vendored/cloudfront-invalidate @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash # Originally from @tsibley's gist: https://gist.github.com/tsibley/a66262d341dedbea39b02f27e2837ea8 set -euo pipefail diff --git a/ingest/bin/csv-to-ndjson b/ingest/vendored/csv-to-ndjson similarity index 66% rename from ingest/bin/csv-to-ndjson rename to ingest/vendored/csv-to-ndjson index 86e84127..84befe08 100755 --- a/ingest/bin/csv-to-ndjson +++ b/ingest/vendored/csv-to-ndjson @@ -1,9 +1,7 @@ #!/usr/bin/env python3 """ -Copied from "bin/csv-to-ndjson" in nextstrain/ncov-ingest: -https://github.com/nextstrain/ncov-ingest/blob/2a5f255329ee5bdf0cabc8b8827a700c92becbe4/bin/csv-to-ndjson - Convert CSV on stdin to NDJSON on stdout. +usage: `cat dummy.csv | ./csv-to-ndjson > dummy.ndjson` """ import csv import json diff --git a/ingest/vendored/docs/ncbi-virus-all-fields-example.json b/ingest/vendored/docs/ncbi-virus-all-fields-example.json new file mode 100644 index 00000000..bbf9a7f7 --- /dev/null +++ b/ingest/vendored/docs/ncbi-virus-all-fields-example.json @@ -0,0 +1,292 @@ +{ + "ExportDate_dt": "2023-08-08T21:02:01.475Z", + "QualNum_i": 0, + "QualPct_d": 0.0, + "IncompleteCdsCnt_i": 0, + "gi_l": 1798174254, + "Host_s": "Homo sapiens", + "HostSpecies_s": "Homo sapiens (human), taxid:9606|", + "HostLineage_ss": [ + "cellular organisms, taxid:131567| biota", + "Eukaryota (eucaryotes), taxid:2759| eukaryotes Eucarya Eucaryotae Eukarya Eukaryotae", + "Opisthokonta, taxid:33154| Fungi/Metazoa group opisthokonts", + "Metazoa (metazoans), taxid:33208| multicellular animals Animalia animals", + "Eumetazoa, taxid:6072|", + "Bilateria, taxid:33213|", + "Deuterostomia (deuterostomes), taxid:33511|", + "Chordata (chordates), taxid:7711|", + "Craniata, taxid:89593|", + "Vertebrata (vertebrates), taxid:7742|", + "Gnathostomata (jawed vertebrates), taxid:7776|", + "Teleostomi, taxid:117570|", + "Euteleostomi (bony vertebrates), taxid:117571|", + "Sarcopterygii, taxid:8287|", + "Dipnotetrapodomorpha, taxid:1338369|", + "Tetrapoda (tetrapods), taxid:32523|", + "Amniota (amniotes), taxid:32524|", + "Mammalia (mammals), taxid:40674|", + "Theria, taxid:32525|", + "Eutheria (placentals), taxid:9347| eutherian mammals placental mammals Placentalia", + "Boreoeutheria, taxid:1437010| Boreotheria", + "Euarchontoglires, taxid:314146|", + "Primates, taxid:9443| Primata primates", + "Haplorrhini, taxid:376913|", + "Simiiformes, taxid:314293| Anthropoidea", + "Catarrhini, taxid:9526|", + "Hominoidea (apes), taxid:314295| ape", + "Hominidae (great apes), taxid:9604| Pongidae", + "Homininae, taxid:207598| Homo/Pan/Gorilla group", + "Homo (humans), taxid:9605|", + "Homo sapiens (human), taxid:9606|" + ], + "HostLineageId_ss": [ + "131567", + "2759", + "33154", + "33208", + "6072", + "33213", + "33511", + "7711", + "89593", + "7742", + "7776", + "117570", + "117571", + "8287", + "1338369", + "32523", + "32524", + "40674", + "32525", + "9347", + "1437010", + "314146", + "9443", + "376913", + "314293", + "9526", + "314295", + "9604", + "207598", + "9605", + "9606" + ], + "Locus_s": "NC_045512", + "OrgId_i": 2697049, + "VirusFamily_s": "Coronaviridae", + "VirusGenus_s": "Betacoronavirus", + "VirusSpecies_s": "Severe acute respiratory syndrome-related coronavirus", + "VirusSpeciesId_i": 694009, + "VirusLineage_ss": [ + "Viruses, taxid:10239| Vira Viridae viruses", + "Riboviria (RNA viruses), taxid:2559587| RNA viruses and viroids", + "Orthornavirae, taxid:2732396|", + "Pisuviricota, taxid:2732408|", + "Pisoniviricetes, taxid:2732506|", + "Nidovirales, taxid:76804|", + "Cornidovirineae, taxid:2499399|", + "Coronaviridae, taxid:11118|", + "Orthocoronavirinae, taxid:2501931|", + "Betacoronavirus, taxid:694002| Coronavirus", + "Sarbecovirus, taxid:2509511|", + "Severe acute respiratory syndrome-related coronavirus, taxid:694009| HCoV-SARS SARS SARSr-CoV SARSrCoV", + "Severe acute respiratory syndrome coronavirus 2, taxid:2697049| SARS-CoV-2", + "RNA viruses" + ], + "VirusLineageId_ss": [ + "10239", + "2559587", + "2732396", + "2732408", + "2732506", + "76804", + "2499399", + "11118", + "2501931", + "694002", + "2509511", + "694009", + "2697049" + ], + "VirusL0_s": "RNA viruses", + "VirusL1_s": "Orthornavirae, taxid:2732396", + "VirusL2_s": "Pisuviricota, taxid:2732408", + "VirusL3_s": "Pisoniviricetes, taxid:2732506", + "VirusL4_s": "Nidovirales, taxid:76804", + "VirusL5_s": "Cornidovirineae, taxid:2499399", + "VirusL6_s": "Coronaviridae, taxid:11118", + "VirusL7_s": "Orthocoronavirinae, taxid:2501931", + "VirusL8_s": "Betacoronavirus, taxid:694002", + "VirusL9_s": "Sarbecovirus, taxid:2509511", + "VirusL10_s": "Severe acute respiratory syndrome-related coronavirus, taxid:694009", + "ViralHost_ss": [ + "human", + "vertebrates" + ], + "GenomicMoltype_s": "ssRNA(+)", + "SLen_i": 29903, + "Flags_ss": [ + "refseq", + "complete" + ], + "Flags_csv": "refseq, complete", + "FlagsCount_i": 2, + "SetAcc_s": "GCF_009858895.2", + "Authors_ss": [ + "Wu,F.", + "Zhao,S.", + "Yu,B.", + "Chen,Y.M.", + "Wang,W.", + "Song,Z.G.", + "Hu,Y.", + "Tao,Z.W.", + "Tian,J.H.", + "Pei,Y.Y.", + "Yuan,M.L.", + "Zhang,Y.L.", + "Dai,F.H.", + "Liu,Y.", + "Wang,Q.M.", + "Zheng,J.J.", + "Xu,L.", + "Holmes,E.C.", + "Zhang,Y.Z.", + "Baranov,P.V.", + "Henderson,C.M.", + "Anderson,C.B.", + "Gesteland,R.F.", + "Atkins,J.F.", + "Howard,M.T.", + "Robertson,M.P.", + "Igel,H.", + "Baertsch,R.", + "Haussler,D.", + "Ares,M. Jr.", + "Scott,W.G.", + "Williams,G.D.", + "Chang,R.Y.", + "Brian,D.A.", + "Chen,Y.-M.", + "Song,Z.-G.", + "Tao,Z.-W.", + "Tian,J.-H.", + "Pei,Y.-Y.", + "Zhang,Y.-L.", + "Dai,F.-H.", + "Wang,Q.-M.", + "Zheng,J.-J.", + "Zhang,Y.-Z." + ], + "Authors_csv": "Wu,F., Zhao,S., Yu,B., Chen,Y.M., Wang,W., Song,Z.G., Hu,Y., Tao,Z.W., Tian,J.H., Pei,Y.Y., Yuan,M.L., Zhang,Y.L., Dai,F.H., Liu,Y., Wang,Q.M., Zheng,J.J., Xu,L., Holmes,E.C., Zhang,Y.Z., Baranov,P.V., Henderson,C.M., Anderson,C.B., Gesteland,R.F., Atkins,J.F., Howard,M.T., Robertson,M.P., Igel,H., Baertsch,R., Haussler,D., Ares,M. Jr., Scott,W.G., Williams,G.D., Chang,R.Y., Brian,D.A., Chen,Y.-M., Song,Z.-G., Tao,Z.-W., Tian,J.-H., Pei,Y.-Y., Zhang,Y.-L., Dai,F.-H., Wang,Q.-M., Zheng,J.-J., Zhang,Y.-Z.", + "AuthorsCount_i": 44, + "Country_s": "China", + "Isolate_s": "Wuhan-Hu-1", + "Lineage_s": "B", + "Division_s": "VRL", + "Keywords_ss": [ + "RefSeq" + ], + "KeywordsCount_i": 1, + "TaxName_s": "Severe acute respiratory syndrome coronavirus 2", + "Region_s": "Asia", + "ParentAcc_s": "set:NC_045512", + "SetPosition_i": 0, + "SourceDB_s": "RefSeq", + "Definition_s": "Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome", + "HostId_i": 9606, + "CreateDate_dt": "2020-01-13T00:00:00Z", + "CreateYear_i": 2020, + "Genome_js": "[{\"id\": \"NC_045512.2\", \"segment\": null, \"proteins\": [{\"id\": \"YP_009724389.1\", \"name\": \"ORF1ab polyprotein\", \"location\": \"join(266..13468,13468..21555)\"}, {\"id\": \"YP_009725295.1\", \"name\": \"ORF1a polyprotein\", \"location\": \"266..13483\"}, {\"id\": \"YP_009724390.1\", \"name\": \"surface glycoprotein\", \"location\": \"21563..25384\"}, {\"id\": \"YP_009724391.1\", \"name\": \"ORF3a protein\", \"location\": \"25393..26220\"}, {\"id\": \"YP_009724392.1\", \"name\": \"envelope protein\", \"location\": \"26245..26472\"}, {\"id\": \"YP_009724393.1\", \"name\": \"membrane glycoprotein\", \"location\": \"26523..27191\"}, {\"id\": \"YP_009724394.1\", \"name\": \"ORF6 protein\", \"location\": \"27202..27387\"}, {\"id\": \"YP_009724395.1\", \"name\": \"ORF7a protein\", \"location\": \"27394..27759\"}, {\"id\": \"YP_009725318.1\", \"name\": \"ORF7b\", \"location\": \"27756..27887\"}, {\"id\": \"YP_009724396.1\", \"name\": \"ORF8 protein\", \"location\": \"27894..28259\"}, {\"id\": \"YP_009724397.2\", \"name\": \"nucleocapsid phosphoprotein\", \"location\": \"28274..29533\"}, {\"id\": \"YP_009725255.1\", \"name\": \"ORF10 protein\", \"location\": \"29558..29674\"}]}]", + "MolType_s": "RNA", + "ProtAcc_ss": [ + "YP_009724389", + "YP_009725295", + "YP_009724390", + "YP_009724391", + "YP_009724392", + "YP_009724393", + "YP_009724394", + "YP_009724395", + "YP_009725318", + "YP_009724396", + "YP_009724397", + "YP_009725255" + ], + "ProtAccCount_i": 12, + "UpdateDate_dt": "2020-07-18T00:00:00Z", + "UpdateYear_i": 2020, + "PubMed_ss": [ + "32015508", + "15680415", + "15630477", + "10482585" + ], + "PubMed_csv": "32015508, 15680415, 15630477, 10482585", + "PubMedCount_i": 4, + "Completeness_s": "complete", + "CountryFull_s": "China", + "ProtNames_ss": [ + "ORF1ab polyprotein", + "ORF1a polyprotein", + "surface glycoprotein", + "ORF3a protein", + "envelope protein", + "membrane glycoprotein", + "ORF6 protein", + "ORF7a protein", + "ORF7b protein", + "ORF8 protein", + "nucleocapsid phosphoprotein", + "ORF10 protein" + ], + "ProtNamesCount_i": 12, + "IsolateParsed_s": "Wuhan-Hu-1", + "NuclAcc_ss": [ + "NC_045512" + ], + "NuclAccCount_i": 1, + "CollectionDate_dr": "2019-12", + "CollectionYear_i": 2019, + "SubmitterAffil_s": "National Center for Biotechnology Information, NIH", + "BioProject_ss": [ + "PRJNA485481" + ], + "BioProject_csv": "PRJNA485481", + "BioProjectCount_i": 1, + "AccVer_s": "NC_045512.2", + "CollectionDate_s": "2019-12", + "SubmitterCountry_s": "USA", + "CollectionDate_dt": "2019-12-01T00:00:00Z", + "GenomeCompleteness_s": "complete", + "SubmitterAffilFull_s": "National Center for Biotechnology Information, NIH", + "BioProject_s": "PRJNA485481", + "AccNV_s": "NC_045512", + "id": "NC_045512", + "SeqType_s": "Nucleotide", + "FastaMD5_s": "4928f859a1822d291e0225206a0068c8", + "live_i": 1, + "ids_ss": [ + "GCF_009858895", + "GCF_009858895.2", + "NC_045512", + "NC_045512.2", + "PRJNA485481", + "YP_009724389", + "YP_009724390", + "YP_009724391", + "YP_009724392", + "YP_009724393", + "YP_009724394", + "YP_009724395", + "YP_009724396", + "YP_009724397", + "YP_009725255", + "YP_009725295", + "YP_009725318", + "set:NC_045512" + ], + "gi_i": 1798174254, + "_version_": 1773711315042304000 +} diff --git a/ingest/vendored/download-from-s3 b/ingest/vendored/download-from-s3 index 44f7ff34..49811863 100755 --- a/ingest/vendored/download-from-s3 +++ b/ingest/vendored/download-from-s3 @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash set -euo pipefail bin="$(dirname "$0")" diff --git a/ingest/vendored/fetch-from-ncbi-entrez b/ingest/vendored/fetch-from-ncbi-entrez new file mode 100755 index 00000000..194a0c81 --- /dev/null +++ b/ingest/vendored/fetch-from-ncbi-entrez @@ -0,0 +1,70 @@ +#!/usr/bin/env python3 +""" +Fetch metadata and nucleotide sequences from NCBI Entrez and output to a GenBank file. +""" +import json +import argparse +from Bio import SeqIO, Entrez + +# To use the efetch API, the docs indicate only around 10,000 records should be fetched per request +# https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch +# However, in my testing with HepB, the max records returned was 9,999 +# - Jover, 16 August 2023 +BATCH_SIZE = 9999 + +Entrez.email = "hello@nextstrain.org" + +def parse_args(): + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument('--term', required=True, type=str, + help='Genbank search term. Replace spaces with "+", e.g. "Hepatitis+B+virus[All+Fields]complete+genome[All+Fields]"') + parser.add_argument('--output', required=True, type=str, help='Output file (Genbank)') + return parser.parse_args() + + +def get_esearch_history(term): + """ + Search for the provided *term* via ESearch and store the results using the + Entrez history server.¹ + + Returns the total count of returned records, query key, and web env needed + to access the records from the server. + + ¹ https://www.ncbi.nlm.nih.gov/books/NBK25497/#chapter2.Using_the_Entrez_History_Server + """ + handle = Entrez.esearch(db="nucleotide", term=term, retmode="json", usehistory="y", retmax=0) + esearch_result = json.loads(handle.read())['esearchresult'] + print(f"Search term {term!r} returned {esearch_result['count']} IDs.") + return { + "count": int(esearch_result["count"]), + "query_key": esearch_result["querykey"], + "web_env": esearch_result["webenv"] + } + + +def fetch_from_esearch_history(count, query_key, web_env): + """ + Fetch records in batches from Entrez history server using the provided + *query_key* and *web_env* and yields them as a BioPython SeqRecord iterator. + """ + print(f"Fetching GenBank records in batches of n={BATCH_SIZE}") + + for start in range(0, count, BATCH_SIZE): + handle = Entrez.efetch( + db="nucleotide", + query_key=query_key, + webenv=web_env, + retstart=start, + retmax=BATCH_SIZE, + rettype="gb", + retmode="text") + + yield SeqIO.parse(handle, "genbank") + + +if __name__=="__main__": + args = parse_args() + + with open(args.output, "w") as output_handle: + for batch_results in fetch_from_esearch_history(**get_esearch_history(args.term)): + SeqIO.write(batch_results, output_handle, "genbank") diff --git a/ingest/vendored/fetch-from-ncbi-virus b/ingest/vendored/fetch-from-ncbi-virus new file mode 100755 index 00000000..39733e6f --- /dev/null +++ b/ingest/vendored/fetch-from-ncbi-virus @@ -0,0 +1,33 @@ +#!/usr/bin/env bash +# usage: fetch-from-ncbi-virus [options] +# +# Fetch metadata and nucleotide sequences from [NCBI Virus](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/) +# and output NDJSON records to stdout. +# +# [options] are passed directly to ncbi-virus-url. See that script for usage details. +# +# Originally copied from "bin/fetch-from-genbank" in nextstrain/ncov-ingest: +# https://github.com/nextstrain/ncov-ingest/blob/2a5f255329ee5bdf0cabc8b8827a700c92becbe4/bin/fetch-from-genbank +# +set -euo pipefail + +bin="$(dirname "$0")" + + +main() { + local ncbi_taxon_id="${1:?NCBI taxon id is required.}" + local github_repo="${2:?A GitHub repository with owner and repository name is required as the second argument}" + + # "${@:3}" represents all other options, if any. + ncbi_virus_url="$("$bin"/ncbi-virus-url --ncbi-taxon-id "$ncbi_taxon_id" "${@:3}")" + + fetch "$ncbi_virus_url" "$github_repo" | "$bin"/csv-to-ndjson +} + +fetch() { + curl "$1" \ + --fail --silent --show-error --http1.1 \ + --header "User-Agent: https://github.com/$2 (hello@nextstrain.org)" +} + +main "$@" diff --git a/ingest/bin/genbank-url b/ingest/vendored/ncbi-virus-url similarity index 63% rename from ingest/bin/genbank-url rename to ingest/vendored/ncbi-virus-url index 7182576d..0dd116b8 100755 --- a/ingest/bin/genbank-url +++ b/ingest/vendored/ncbi-virus-url @@ -1,7 +1,7 @@ #!/usr/bin/env python3 """ -Generate URL to download all mpox virus sequences and their curated metadata -from GenBank via NCBI Virus. +Generate URL to download all virus sequences and their curated metadata for a +specified NCBI Taxon ID from GenBank via NCBI Virus. The URL this program builds is based on the URL for SARS-CoV-2 constructed with @@ -9,25 +9,31 @@ The URL this program builds is based on the URL for SARS-CoV-2 constructed with and observing the network activity at - https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Monkeypox%20virus,%20taxid:10244 + https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide """ from urllib.parse import urlencode +from typing import List, Optional import argparse def parse_args(): - parser = argparse.ArgumentParser( - description="Given an NCBI taxon ID, generate URL to download " - "all viral sequences and their curated metadata from GenBank via NCBI Virus." - ) - parser.add_argument( - "--ncbi-taxon-id", - help="NCBI Taxon ID.", - default="10244", - required=True - ) + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--ncbi-taxon-id", required=True, + help="NCBI Taxon ID. Visit NCBI virus at " + + "https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/find-data/virus " + + "to search for supported taxon IDs.") + parser.add_argument("--filters", required=False, nargs="*", + help="Filter criteria to add as `fq` param values. " + + "Apply filters via the NCBI Virus UI and observe the network " + + "activity to find the desired filter string.") + parser.add_argument("--fields", required=False, nargs="*", + help="Metadata fields to add as `fl` param values. " + + "Expected to be formatted as :. " + + "See docs/ncbi-virus-all-fields-example.json for the available NCBI Virus fields.") return parser.parse_args() -def build_query_url(ncbi_taxon_id: str): +def build_query_url(ncbi_taxon_id: str, + filters: Optional[List[str]]=None, + fields: Optional[List[str]]=None): """ Generate URL to download all viral sequences and their curated metadata from GenBank via NCBI Virus. @@ -37,7 +43,8 @@ def build_query_url(ncbi_taxon_id: str): # Search criteria 'fq': [ '{!tag=SeqType_s}SeqType_s:("Nucleotide")', # Nucleotide sequences (as opposed to protein) - f'VirusLineageId_ss:({ncbi_taxon_id})', # NCBI Taxon id for Monkeypox + f'VirusLineageId_ss:({ncbi_taxon_id})', + *(filters or []), ], # Unclear, but seems necessary. @@ -47,7 +54,7 @@ def build_query_url(ncbi_taxon_id: str): 'cmd': 'download', 'dlfmt': 'csv', 'fl': ','.join( - ':'.join(names) for names in [ + [':'.join(names) for names in [ # Pairs of (output column name, source data field). ('genbank_accession', 'id'), ('genbank_accession_rev', 'AccVer_s'), @@ -57,6 +64,7 @@ def build_query_url(ncbi_taxon_id: str): ('location', 'CountryFull_s'), ('collected', 'CollectionDate_s'), ('submitted', 'CreateDate_dt'), + ('updated', 'UpdateDate_dt'), ('length', 'SLen_i'), ('host', 'Host_s'), ('isolation_source', 'Isolation_csv'), @@ -68,7 +76,7 @@ def build_query_url(ncbi_taxon_id: str): ('submitting_organization', 'SubmitterAffilFull_s'), ('publications', 'PubMed_csv'), ('sequence', 'Nucleotide_seq'), - ] + ]] + (fields or []) ), # Stable sort with GenBank accessions. @@ -85,7 +93,11 @@ def build_query_url(ncbi_taxon_id: str): def main(): args = parse_args() - build_query_url(args.ncbi_taxon_id) + build_query_url( + ncbi_taxon_id=args.ncbi_taxon_id, + filters=args.filters, + fields=args.fields + ) if __name__ == '__main__': main() diff --git a/ingest/vendored/notify-on-diff b/ingest/vendored/notify-on-diff index c304d6b5..ddbe7da0 100755 --- a/ingest/vendored/notify-on-diff +++ b/ingest/vendored/notify-on-diff @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash set -euo pipefail diff --git a/ingest/vendored/notify-on-job-fail b/ingest/vendored/notify-on-job-fail index 02cb6bad..7dd24095 100755 --- a/ingest/vendored/notify-on-job-fail +++ b/ingest/vendored/notify-on-job-fail @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash set -euo pipefail : "${SLACK_TOKEN:?The SLACK_TOKEN environment variable is required.}" diff --git a/ingest/vendored/notify-on-job-start b/ingest/vendored/notify-on-job-start index 3e44bb09..1c8ce7d6 100755 --- a/ingest/vendored/notify-on-job-start +++ b/ingest/vendored/notify-on-job-start @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash set -euo pipefail : "${SLACK_TOKEN:?The SLACK_TOKEN environment variable is required.}" diff --git a/ingest/vendored/notify-on-record-change b/ingest/vendored/notify-on-record-change index c0bf8f7e..f424252c 100755 --- a/ingest/vendored/notify-on-record-change +++ b/ingest/vendored/notify-on-record-change @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash set -euo pipefail : "${SLACK_TOKEN:?The SLACK_TOKEN environment variable is required.}" diff --git a/ingest/vendored/notify-slack b/ingest/vendored/notify-slack index db98bfb8..a343435f 100755 --- a/ingest/vendored/notify-slack +++ b/ingest/vendored/notify-slack @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash set -euo pipefail : "${SLACK_TOKEN:?The SLACK_TOKEN environment variable is required.}" diff --git a/ingest/vendored/s3-object-exists b/ingest/vendored/s3-object-exists index faac4219..679c20a3 100755 --- a/ingest/vendored/s3-object-exists +++ b/ingest/vendored/s3-object-exists @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash set -euo pipefail url="${1#s3://}" diff --git a/ingest/vendored/tests/fetch-from-ncbi-virus/filter-and-fields.t b/ingest/vendored/tests/fetch-from-ncbi-virus/filter-and-fields.t new file mode 100644 index 00000000..2fd7020f --- /dev/null +++ b/ingest/vendored/tests/fetch-from-ncbi-virus/filter-and-fields.t @@ -0,0 +1,18 @@ +Get the virus lineage IDs for 4 early Dengue sequences, testing the options --filter and --field. + + $ $TESTDIR/../../fetch-from-ncbi-virus 12637 nextstrain/ingest \ + > --filters 'CreateDate_dt:([1987-11-29T00:00:00Z TO 1987-11-29T00:00:01Z])' \ + > --fields 'viruslineage_ids:VirusLineageId_ss' + {"genbank_accession":"X05375","genbank_accession_rev":"X05375.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for envelope protein E N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"GTAACTTATGGGACGTGTACCACCACAGGAGAACACAGAAGAGAAAAAAGATCAGTGGCACTCGTTCCACATGTGGGAATGGGACTGGAGACACGAACTGAAACATGGATGTCATCAGAAGGGGCCTGGAAACATGCCCAGAGAATTGAAACTTGGATCTTGAGACATCCAGGCTTTACCATAATGGCAGCAATCCTGGCATACACCATAGGAACGACACATTTCCAAAGAGCCCTGATTTTCATCTTACTGACAGCTGTCGCTCCTTCAATGACAATGCGTTGCATAGGAATATCAAATAGAGACTTTGTAGAAGGGGTTTCAGGAGGAAGCTGGGTTGACATAGTCTTAGAACATGGA","viruslineage_ids":"10239,2559587,2732396,2732406,2732462,2732545,11050,11051,12637,11060"} + {"genbank_accession":"X05376","genbank_accession_rev":"X05376.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for NS1 protein N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"ACAACAATGAGGGGAGCGAAGAGAATGGCCATTTTAGGTGACACAGCTTGGGATTTTGGATCCCTGGGAGGAGTGTTTACATCTATAGGAAAGGCTCTCCACCAAGTTTTCGGAGCAATCTATGGGGCTGCCTTCAGTGGGGTCTCATGGACTATGAAAATCCTCATAGGAGTCATTATCACATGGATAGGAATGAATTCACGCAGCACCTCACTTTCTGTGTCACTAGTATTGGTGGGAGTCGTGACGCTGTATTTGGGAGTTATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAAAACAAAGAACTGAAGTGTGGCAGTGGGATTTTCATCACAGACAACGTGCACACATGG","viruslineage_ids":"10239,2559587,2732396,2732406,2732462,2732545,11050,11051,12637,11060"} + {"genbank_accession":"X05377","genbank_accession_rev":"X05377.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for NS3 protein N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"CTCACTGTGTGCTACGTGCTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCCGCCGATGTCAAATGGGAAGATCAGGCAGAGATATCAGGAAGCAGTCCAATCCTGTCAATAACAATATCAGAAGATGGTAGCATGTCGATAAAAAACGAAGAGGAAGAACAAACACTGACCATACTCATTAGAACAGGATTGCTGGTGATCTCAGGACTTTTTCCTGTATCAATACCAATCACGGCAGCAGCATGGTACCTGTGGGAAGTGAAGAAACAACGGGCTGGAGTATTGTGGGATGTCCCTTCACCCCCACCCGTGGGAAAGGCTGAACTGGAAGATGGAGCCTATAGAATCAAGCAA","viruslineage_ids":"10239,2559587,2732396,2732406,2732462,2732545,11050,11051,12637,11060"} + {"genbank_accession":"X05378","genbank_accession_rev":"X05378.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for NS5 protein N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"GATCCAATACCCTATGATCCAAAGTTTGAAAAGCAGTTGGGACAAGTAATGCTCCTAGTCCTCTGCGGGACTCAAGTGTTGATGATGAGGACTACATGGGCTCTGTGTGAGGCTTTAACCTTAGCGACCGGGCCTATCTCCACATTGTGGGAAGGAAATCCAGGGAGGTTTTGGAACACTACCATTGCAGTGTCAATGGCTAACATTTTTAGAGGGAGTTACTTGGCCGGAGCTGGACTTCTCTTTTCCATCATGAAGAACACAACCAACACGAGAAGGGGAACTGGCAACATAGGAGAGACGCTTGGAGAGAAATGGAAAAGCCGATTGAACGCATTGGGGAAAAGTGAATTCCAGATC","viruslineage_ids":"10239,2559587,2732396,2732406,2732462,2732545,11050,11051,12637,11060"} + +Do the same but without --field. + + $ $TESTDIR/../../fetch-from-ncbi-virus 12637 nextstrain/ingest \ + > --filters 'CreateDate_dt:([1987-11-29T00:00:00Z TO 1987-11-29T00:00:01Z])' + {"genbank_accession":"X05375","genbank_accession_rev":"X05375.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for envelope protein E N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"GTAACTTATGGGACGTGTACCACCACAGGAGAACACAGAAGAGAAAAAAGATCAGTGGCACTCGTTCCACATGTGGGAATGGGACTGGAGACACGAACTGAAACATGGATGTCATCAGAAGGGGCCTGGAAACATGCCCAGAGAATTGAAACTTGGATCTTGAGACATCCAGGCTTTACCATAATGGCAGCAATCCTGGCATACACCATAGGAACGACACATTTCCAAAGAGCCCTGATTTTCATCTTACTGACAGCTGTCGCTCCTTCAATGACAATGCGTTGCATAGGAATATCAAATAGAGACTTTGTAGAAGGGGTTTCAGGAGGAAGCTGGGTTGACATAGTCTTAGAACATGGA"} + {"genbank_accession":"X05376","genbank_accession_rev":"X05376.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for NS1 protein N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"ACAACAATGAGGGGAGCGAAGAGAATGGCCATTTTAGGTGACACAGCTTGGGATTTTGGATCCCTGGGAGGAGTGTTTACATCTATAGGAAAGGCTCTCCACCAAGTTTTCGGAGCAATCTATGGGGCTGCCTTCAGTGGGGTCTCATGGACTATGAAAATCCTCATAGGAGTCATTATCACATGGATAGGAATGAATTCACGCAGCACCTCACTTTCTGTGTCACTAGTATTGGTGGGAGTCGTGACGCTGTATTTGGGAGTTATGGTGCAGGCCGATAGTGGTTGCGTTGTGAGCTGGAAAAACAAAGAACTGAAGTGTGGCAGTGGGATTTTCATCACAGACAACGTGCACACATGG"} + {"genbank_accession":"X05377","genbank_accession_rev":"X05377.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for NS3 protein N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"CTCACTGTGTGCTACGTGCTCACTGGACGATCGGCCGATTTGGAACTGGAGAGAGCCGCCGATGTCAAATGGGAAGATCAGGCAGAGATATCAGGAAGCAGTCCAATCCTGTCAATAACAATATCAGAAGATGGTAGCATGTCGATAAAAAACGAAGAGGAAGAACAAACACTGACCATACTCATTAGAACAGGATTGCTGGTGATCTCAGGACTTTTTCCTGTATCAATACCAATCACGGCAGCAGCATGGTACCTGTGGGAAGTGAAGAAACAACGGGCTGGAGTATTGTGGGATGTCCCTTCACCCCCACCCGTGGGAAAGGCTGAACTGGAAGATGGAGCCTATAGAATCAAGCAA"} + {"genbank_accession":"X05378","genbank_accession_rev":"X05378.1","database":"GenBank","strain":"","region":"","location":"","collected":"","submitted":"1987-11-29T00:00:00Z","updated":"2016-07-26T00:00:00Z","length":"360","host":"","isolation_source":"","bioproject_accession":"","biosample_accession":"","sra_accession":"","title":"Dengue virus type 2 genomic RNA for NS5 protein N-term","authors":"Biedrzycka,A., Cauchi,M.R., Bartholomeusz,A., Gorman,J.J., Wright,P.J.","submitting_organization":"","publications":"2952760","sequence":"GATCCAATACCCTATGATCCAAAGTTTGAAAAGCAGTTGGGACAAGTAATGCTCCTAGTCCTCTGCGGGACTCAAGTGTTGATGATGAGGACTACATGGGCTCTGTGTGAGGCTTTAACCTTAGCGACCGGGCCTATCTCCACATTGTGGGAAGGAAATCCAGGGAGGTTTTGGAACACTACCATTGCAGTGTCAATGGCTAACATTTTTAGAGGGAGTTACTTGGCCGGAGCTGGACTTCTCTTTTCCATCATGAAGAACACAACCAACACGAGAAGGGGAACTGGCAACATAGGAGAGACGCTTGGAGAGAAATGGAAAAGCCGATTGAACGCATTGGGGAAAAGTGAATTCCAGATC"} diff --git a/ingest/vendored/tests/fetch-from-ncbi-virus/invalid-taxon-id.t b/ingest/vendored/tests/fetch-from-ncbi-virus/invalid-taxon-id.t new file mode 100644 index 00000000..7a0d5223 --- /dev/null +++ b/ingest/vendored/tests/fetch-from-ncbi-virus/invalid-taxon-id.t @@ -0,0 +1,4 @@ +Fetch from an invalid Taxon ID without any additional options. +This should not error nor return any output. + + $ $TESTDIR/../../fetch-from-ncbi-virus INVALID_TAXID nextstrain/ingest diff --git a/ingest/vendored/trigger b/ingest/vendored/trigger index 11d1b635..586f9cc0 100755 --- a/ingest/vendored/trigger +++ b/ingest/vendored/trigger @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash set -euo pipefail : "${PAT_GITHUB_DISPATCH:=}" diff --git a/ingest/vendored/trigger-on-new-data b/ingest/vendored/trigger-on-new-data index ef71d88d..470d2f4f 100755 --- a/ingest/vendored/trigger-on-new-data +++ b/ingest/vendored/trigger-on-new-data @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash set -euo pipefail : "${PAT_GITHUB_DISPATCH:?The PAT_GITHUB_DISPATCH environment variable is required.}" diff --git a/ingest/vendored/upload-to-s3 b/ingest/vendored/upload-to-s3 index 31cd49bf..36d171c6 100755 --- a/ingest/vendored/upload-to-s3 +++ b/ingest/vendored/upload-to-s3 @@ -1,4 +1,4 @@ -#!/bin/bash +#!/usr/bin/env bash set -euo pipefail bin="$(dirname "$0")" diff --git a/ingest/workflow/snakemake_rules/fetch_sequences.smk b/ingest/workflow/snakemake_rules/fetch_sequences.smk index 6a5df856..aea03475 100644 --- a/ingest/workflow/snakemake_rules/fetch_sequences.smk +++ b/ingest/workflow/snakemake_rules/fetch_sequences.smk @@ -20,7 +20,7 @@ rule fetch_from_genbank: retries: 5 # Requires snakemake 7.7.0 or later shell: """ - ./bin/fetch-from-genbank 10244 > {output.genbank_ndjson} + ./vendored/fetch-from-ncbi-virus 10244 nextstrain/monkeypox > {output.genbank_ndjson} """