viralfetch 0.1.3

The VMR is the local index; remote sources are fetched on demand and cached.

Installation

pip install viralfetch

This installs the viralfetch command and everything it needs in one step — including Pillow (for drawing chapter figures) and alv/Biopython (for the alignment viewer). Python 3.10+ is required.

NCBI configuration

Commands that reach NCBI (seq, tax --ncbi, tax --compare-ncbi, text, update) 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.

Session vs. persisted. An export (or --email) applies only to the current shell session. To store the email permanently, use:

viralfetch config --store-ncbi-email you@example.com

This writes to the config file (see viralfetch config), which survives across sessions. Running viralfetch config warns you when no email is persisted yet.

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 --ncbi (remote)

Look the lineage up directly in NCBI's taxonomy database instead of the local VMR — useful for a name the VMR does not carry (a non-viral host, a very recent taxon, an NCBI synonym). The name is resolved to a taxid via esearch, then its lineage is fetched. Requires an NCBI email (see above).

viralfetch tax "SARS-CoV-2" --ncbi

╭─ SARS-CoV-2  (species) ────────────────────────╮
│ lineage                                        │
│ └── realm: Riboviria                           │
│     └── … → family: Coronaviridae              │
│         └── species: SARS-CoV-2                │
╰────────────────────────────────────────────────╯
NCBI taxonomy — taxid 2697049

With --json the payload is {source: "ncbi", taxid, name, rank, lineage}. An unknown name exits 1. --ncbi and --compare-ncbi are mutually exclusive.

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. Figures are kept as image links; --images also draws them in the terminal (see below).

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, images, markdown} instead — images is a list of {url, alt} for the chapter's figures, whose absolute URLs also appear inline in the Markdown as ![alt](url).

Figures in the terminal

--images draws the chapter's figures in their original place in the text, as truecolor Unicode block-element graphics sized to your terminal (full width by default, for the sharpest picture). Each character cell packs a 2×2 grid of sub-pixels with a per-cell best-fit of two colours; the image is downscaled in linear light (LANCZOS) and error-diffusion dithered, so gradients stay smooth. It renders the same on any truecolor terminal — no special graphics protocol required. Each figure keeps its alt as a caption. It applies only to the interactive Rich view (not --raw, --json, or when piped):

viralfetch text Coronaviridae --images
viralfetch text Coronaviridae --images --fig-width 60   # cap the size

Figures are fetched politely (rate-limited, robots.txt-honouring, from the ICTV domain only) and cached permanently. A missing or broken figure is skipped, never fatal.

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

Names the VMR doesn't know fall back to NCBI

If a name is absent from the local VMR, text asks NCBI taxonomy for its family before giving up, and — if NCBI places it in one — shows that family's chapter (with a note on stderr). This catches recent taxa and NCBI synonyms the bundled VMR predates:

viralfetch text "some-recent-virus"
# stderr: 'some-recent-virus' is not in the local VMR; NCBI places it in
#         family Rhabdoviridae — showing that chapter.
# stdout: the Rhabdoviridae chapter

The fallback is best-effort: if NCBI is unreachable or knows no family, the name is tried verbatim and, failing that, 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.

tree — phylogenetic tree (local, NCBI only as a fallback)

Show the ICTV Report phylogenetic tree for a taxon's family, drawn as an indented cladogram. Trees are bundled locally (Newick + metadata + a tip→virus table per family), so this works offline.

The name is resolved through the VMR to its family, and the tip(s) it points at are highlighted: a species highlights its own tip, a genus its whole clade, a family shows the tree with nothing highlighted. A name the VMR does not know is searched for among every tree's members (so a virus member name that is not an ICTV taxon still finds its tree).

Failing that, the name is looked up in NCBI taxonomy — which knows strains, synonyms and taxa newer than the bundled VMR. Its lineage names the family (the same family names ICTV uses), and the deepest rank the trees do record — species → subgenus → genus → subfamily — highlights the query's closest relatives on that tree. The note on stderr always says which rank was used:

viralfetch tree "Dengue virus 2"
# 'Dengue virus 2' is not in the local VMR; NCBI places it in family
# Flaviviridae — no tip matches 'dengue virus type 2' itself, so its subgenus
# 'Euflavivirus' is highlighted instead (closest relatives on the tree).

This step is the only one that touches the network, and it is best-effort: with no NCBI email configured (viralfetch config --store-ncbi-email you@example.com) or no connection it is silently skipped, leaving the offline behaviour intact. msa resolves names the same way.

viralfetch tree "Betacoronavirus pandemicum"

Coronaviridae · Figure 5A · RdRp (AA) · maximum likelihood · 55 tips · 2 matches
     ┌─ Alphacoronavirus BT020
   ┌─┤
   │ └─ Scotophilus bat coronavirus 512
  ─┤          …
   │     ┌ severe acute respiratory syndrome coronavirus  ← match
   └─────┤
         └ severe acute respiratory syndrome coronavirus 2  ← match

Caption: Figure 5 Coronaviridae. Phylogenetic relationships among members …
Other trees for Coronaviridae: --tree 2 (helicase)

When a family has several trees, pick one with --tree N; the query defaults to whichever tree contains the match. Other options:

--newick and --json keep stdout clean (the redirect note goes to stderr). With --json, the command emits {family, source, note, matched_rank, matched_value, tree: {…, matched, newick}, other_trees} — source is vmr, member or ncbi, and matched_rank/matched_value say what the highlight fell back to. An unknown name gets "did you mean" suggestions and exit code 1; a family with no bundled tree exits 1 with a note.

msa — multiple sequence alignment (local, no network)

Show the alignment behind a family's tree — the aligned FASTA that sits beside each Newick — coloured by residue and wrapped into blocks with a column ruler (via alv). The name is resolved to its family exactly as tree does, and the query's own records are marked ▶.

The alignments run to thousands of columns, so the view defaults to a leading column window that fits your terminal; move or widen it with --range.

viralfetch msa "Betacoronavirus pandemicum" --consensus

Coronaviridae · tree1 · AA · cols 1–60 of 316 · 55 seqs · 2 matches
consensus              KHFFFAQDGDAAITDYDYYRYNRPTMLDICQALFVYEVVDKYFDIYEGGCITAKEVVVTN
▶ severe acute respir  KHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNN
Alphapironavirus bona  EHFFYLQPRDCAVTDFDYYRFNRPTVLDPLQFRFVYNVVKHYFKSYSAGCLKSEFVIINN
…                      0^                 20^                 40^

With --json, the command emits {family, tree_id, molecule, total_cols, start, n_cols, matched, consensus, rows: [{name, seq, matched}]}. A family whose tree has no bundled alignment exits 1 with a note.

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
                                    # (warns if no NCBI email is persisted yet)
viralfetch config --store-ncbi-email you@example.com    # persist email
viralfetch config --store-ncbi-apikey KEY               # persist API key
viralfetch cache info               # per-namespace entry counts and size
viralfetch cache clear --texts      # drop cached ICTV chapters (or --seqs, --images, 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, and chapter figures) 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.