viralfetch 0.1.0

The VMR is the local index; everything else is fetched on demand and cached.

Installation

pip install -e .

This installs the viralfetch command. Python 3.10+ is required.

NCBI configuration

Commands that reach NCBI (seq, tax --compare-ncbi) require a real email address, per NCBI usage policy. There is no default — the command fails with an explanation if none is set.

export NCBI_EMAIL="you@example.com"
export NCBI_API_KEY="..."   # optional; raises the rate limit from 3 to 10 req/s

You can also pass --email / --api-key on any command.

Global options

These go before the command:

Run viralfetch COMMAND --help to see a command's own arguments and options.

tax — taxonomy lineage (local)

Show the full ICTV lineage of a taxon (realm → species). Case-insensitive, with "did you mean" suggestions on a near miss. A species also gets an isolate summary.

viralfetch tax Coronaviridae

╭─ Coronaviridae  (family) ─────────────────────────╮
│ lineage                                           │
│ └── realm: Riboviria                              │
│     └── kingdom: Orthornavirae                    │
│         └── phylum: Pisuviricota                  │
│             └── class: Pisoniviricetes            │
│                 └── order: Nidovirales            │
│                     └── suborder: Cornidovirineae │
│                         └── family: Coronaviridae │
╰───────────────────────────────────────────────────╯

Same query as JSON:

viralfetch --json tax Coronaviridae

{
  "name": "Coronaviridae",
  "rank": "family",
  "lineage": {
    "realm": "Riboviria",
    "kingdom": "Orthornavirae",
    "phylum": "Pisuviricota",
    "class": "Pisoniviricetes",
    "order": "Nidovirales",
    "suborder": "Cornidovirineae",
    "family": "Coronaviridae"
  }
}

tax --compare-ncbi (remote)

Fetch the NCBI taxonomy lineage for a representative accession and render it beside the ICTV lineage, highlighting divergences. Divergences are expected — NCBI commonly lags ICTV — and are the point of the command.

viralfetch tax "Betacoronavirus pandemicum" --compare-ncbi

             ICTV vs NCBI lineage — Betacoronavirus pandemicum
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ ICTV (VMR)                          ┃ NCBI (taxid 227984)                ┃
┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ realm: Riboviria                    │ acellular root: Viruses            │
│ kingdom: Orthornavirae              │ realm: Riboviria                   │
│ …                                   │ …                                  │
│ species: Betacoronavirus pandemicum │ species: Betacoronavirus pandemi…  │
│                                     │ no rank: SARS coronavirus Tor2     │
└─────────────────────────────────────┴────────────────────────────────────┘

members — child taxa (local, no network)

List the taxa below a given taxon.

At a specific rank

viralfetch members Coronaviridae --rank genus

genera in family Coronaviridae
┏━━━━━━━━━━━━━━━━━━┳━━━━━━━━━┓
┃ genus            ┃ species ┃
┡━━━━━━━━━━━━━━━━━━╇━━━━━━━━━┩
│ Alphacoronavirus │      26 │
│ Alphaletovirus   │       1 │
│ Alphapironavirus │       1 │
│ Betacoronavirus  │      14 │
│ Deltacoronavirus │       7 │
│ Gammacoronavirus │       5 │
└──────────────────┴─────────┘
           6 genera

Counts only

viralfetch members Riboviria --rank family --count

158 families in realm Riboviria

Per-rank breakdown (no flags)

viralfetch members Coronaviridae

  members of family
Coronaviridae by rank
┏━━━━━━━━━━━┳━━━━━━━┓
┃ rank      ┃ count ┃
┡━━━━━━━━━━━╇━━━━━━━┩
│ subfamily │     3 │
│ genus     │     6 │
│ subgenus  │    28 │
│ species   │    54 │
└───────────┴───────┘
Tip: add --tree to list every member of Coronaviridae as a hierarchy.

Full descendant tree

viralfetch members Coronaviridae --tree

Coronaviridae  (family)
├── Letovirinae  (subfamily)
│   └── Alphaletovirus  (genus)
│       └── Milecovirus  (subgenus)
│           └── Alphaletovirus microhylae  (species)
├── Orthocoronavirinae  (subfamily)
│   ├── Alphacoronavirus  (genus)
│   │   ├── Amalacovirus  (subgenus)
│   │   │   └── Alphacoronavirus almalfi  (species)
│   │   └── …
│   └── …
└── …
91 descendant taxa

--rank, --tree, and the breakdown all work with --json too.

seq — NCBI sequence data (remote)

Accessions are resolved locally from the VMR, then metadata or records are fetched from NCBI. Output formats are mutually exclusive; --meta is the default.

Metadata for a species

viralfetch seq "Betacoronavirus pandemicum" --meta

             nuccore metadata — Betacoronavirus pandemicum
┏━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┳━━━━━━━━━┳━━━━━━━━━┳━━━┈
┃ accession  ┃ organism            ┃   len ┃ moltype ┃ biomol  ┃ …
┡━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━╇━━━━━━━━━╇━━━━━━━━━╇━━━┈
│ AY274119.3 │ SARS coronavirus…   │ 29751 │ rna     │ genomic │ …
│ AY613950.1 │ SARS coronavirus…   │ 29728 │ rna     │ genomic │ …
│ MN908947.3 │ SARS-CoV-2 Wuhan-…  │ 29903 │ rna     │ genomic │ …
│ KY352407.1 │ SARS-related coro…  │ 29274 │ rna     │ genomic │ …
└────────────┴─────────────────────┴───────┴─────────┴─────────┴───┈

(Columns topology, completeness, sourcedb and updatedate are shown too; trimmed here for width. Add --json for the full, untruncated records.)

Download FASTA to a file

viralfetch seq "Betacoronavirus pandemicum" --fasta -o out.fa

Wrote 4 fasta record(s) for Betacoronavirus pandemicum to out.fa

Without -o, records go to stdout (pipeable), and the summary goes to stderr.

A whole taxon

--taxon operates on every species beneath a taxon. With --meta it shows a local aggregate (no network) so you can decide whether a download is worth it:

viralfetch seq --taxon Coronaviridae --meta

╭─ Coronaviridae (family) — download estimate ─╮
│ species     54                               │
│ isolates    59                               │
│ accessions  59                               │
│ RefSeq       0                               │
╰──────────────────────────────────────────────╯
   by genome composition
┏━━━━━━━━━━━━━┳━━━━━━━━━━━━┓
┃ composition ┃ accessions ┃
┡━━━━━━━━━━━━━╇━━━━━━━━━━━━┩
│ ssRNA(+)    │         59 │
└─────────────┴────────────┘

{
  "name": "Coronaviridae",
  "rank": "family",
  "species": 54,
  "isolates": 59,
  "accessions": 59,
  "refseq": 0,
  "moltype_breakdown": { "ssRNA(+)": 59 }
}

Fetches of more than 500 accessions ask for confirmation unless --yes is given (in --json / non-interactive mode they refuse without --yes).

Molecule selection

--moltype and --biomol are db=nuccore fields, filtered locally over the metadata (matching is lenient — --moltype ssRNA matches ss-RNA):

viralfetch seq --taxon Filoviridae --moltype ssRNA --fasta -o filo.fa
viralfetch seq "Betacoronavirus pandemicum" --biomol genomic

--protein is a separate path, not a nuccore filter: proteins live in db=protein, reached via elink (nuccore → protein).

viralfetch seq "Betacoronavirus pandemicum" --protein --fasta

text — ICTV Report chapter (remote)

Fetch the ICTV Report chapter for a family, convert its main content to Markdown, and render it with headings, subsection titles, characteristic tables, and the italics of scientific names preserved. The original page URL and the chapter's references/attribution are shown at the top, and the content is CC BY 4.0. Images are omitted.

viralfetch text Coronaviridae

                          Family: Coronaviridae

Source: https://ictv.global/report/chapter/coronaviridae/coronaviridae

Patrick C.Y. Woo, Raoul J. de Groot, Bart Haagmans, Susanna K.P. Lau, …

The citation for this ICTV Report chapter is the summary published as:
Woo et al., (2023), ICTV Virus Taxonomy Profile: Coronaviridae 2023,
Journal of General Virology (2023) 104, 001843

Content is licensed CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/).
────────────────────────────────────────────────────────────────────────
Summary

Members of the family Coronaviridae, a monophyletic group of viruses in
the order Nidovirales, are enveloped, positive-sense RNA viruses …

A single section

--section restricts the output to one section, matched by heading (case-insensitive substring). The top attribution block is always kept.

viralfetch text Coronaviridae --section summary

Raw Markdown to a file

--raw emits the pure Markdown (no Rich decoration), ready to redirect:

viralfetch text Geminiviridae --raw > geminiviridae.md

# Family: Geminiviridae

*Source: https://ictv.global/report/chapter/geminiviridae/geminiviridae*

**Elvira Fiallo-Olivé, Jean-Michel Lett, Darren P. Martin, …**

The citation for this ICTV Report chapter is the summary published as
Fiallo-Olivé et al., ICTV Virus Taxonomy Profile: *Geminiviridae* 2021, …

With --json, the command emits {slug, title, url, doi, markdown} instead.

Genera and species resolve to their family chapter

The ICTV Report is organised by family — genera and species have no chapter of their own. Given one, text looks it up in the VMR and shows its family's chapter, with a note on stderr (so --raw/--json stdout stays clean):

viralfetch text Betacoronavirus
# stderr: 'Betacoronavirus' is a genus; the ICTV Report has no genus chapter
#         — showing its family, Coronaviridae.
# stdout: the Coronaviridae chapter

An unknown name gets "did you mean" suggestions and exit code 1.

Fetching honours ictv.global/robots.txt, sends a descriptive User-Agent carrying your contact email, waits at least 1 second between requests, and caches chapter HTML for 30 days.

Utilities

Small helper commands, all local except update.

viralfetch diagnose                 # VMR parser quality (zero-accession rows)
viralfetch update                   # is a newer VMR published on ictv.global?
viralfetch config                   # show email, masked API key, cache paths
viralfetch config --store-ncbi-email you@example.com   # persist credentials
viralfetch cache info               # per-namespace entry counts and size
viralfetch cache clear --texts      # drop cached ICTV chapters (or --seqs, or all)

diagnose reports the parser's quality indicator — how many VMR rows yielded zero accessions:

╭─ VMR accession-parser diagnostics ─╮
│ isolates              19271        │
│ accessions            23249        │
│ empty-accession rows  141          │
│ unparsed rows         0            │
╰────────────────────────────────────╯

Shell completion: taxon names complete from the VMR (viralfetch tax Corona<TAB> → Coronaviridae). Install it once with viralfetch --install-completion.

Output & exit codes

• Rich tables/panels/trees by default; --json for clean, jq-ready output. Colour is disabled automatically when stdout is not a TTY.
• Errors go to stderr with a non-zero exit code: 1 not found, 2 bad usage, 3 missing NCBI email, 4 NCBI request failed.
• Partial failures are reported, never swallowed: if you request 200 accessions and 197 come back, the 3 missing ones are listed.

Caching

Immutable data (sequences, accession metadata) is cached permanently; ICTV chapter HTML uses a 30-day TTL. The cache lives in the platform cache directory. Use --no-cache to bypass it for a single run.