diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 30403d5..f45b692 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -13,6 +13,16 @@ jobs: steps: - name: Checkout uses: actions/checkout@v4 + - name: Setup Miniconda (for Pyodide world build) + uses: conda-incubator/setup-miniconda@v3 + with: + auto-activate-base: true + - name: Install Rust (for Pyodide world build) + run: | + if ! command -v rustup >/dev/null 2>&1; then + curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y + echo "$HOME/.cargo/bin" >> "$GITHUB_PATH" + fi - name: Setup Python uses: actions/setup-python@v5 with: @@ -20,6 +30,15 @@ jobs: - name: Install the dependencies run: | python -m pip install -r requirements.txt + - name: Build the Pyodide world + run: | + ./build_pyodide_world.sh - name: Build the JupyterLite site run: | ./build.sh + - name: Install test dependencies + run: | + python -m pip install nbclient nbformat pytest tszip==0.2.6 sc2ts + - name: Run notebook tests + run: | + pytest tests/test_notebooks_pyodide.py diff --git a/.gitignore b/.gitignore index b661992..0a764a4 100644 --- a/.gitignore +++ b/.gitignore @@ -1,116 +1 @@ -*.bundle.* -lib/ -node_modules/ -.yarn-packages/ -*.egg-info/ -.ipynb_checkpoints -*.tsbuildinfo - -# Created by https://www.gitignore.io/api/python -# Edit at https://www.gitignore.io/?templates=python - -### Python ### -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -pip-wheel-metadata/ -share/python-wheels/ -.installed.cfg -*.egg -MANIFEST - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.nox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -.hypothesis/ -.pytest_cache/ - -# Translations -*.mo -*.pot - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -target/ - -# pyenv -.python-version - -# celery beat schedule file -celerybeat-schedule - -# SageMath parsed files -*.sage.py - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# Mr Developer -.mr.developer.cfg -.project -.pydevproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ -.dmypy.json -dmypy.json - -# Pyre type checker -.pyre/ - -# OS X stuff -*.DS_Store - -# End of https://www.gitignore.io/api/python - -# jupyterlite -*.doit.db -_output +env diff --git a/README.md b/README.md index d2c622a..ac8ac37 100644 --- a/README.md +++ b/README.md @@ -34,4 +34,28 @@ optional utilities and extensions to make the JupyterLite experience more enjoya For a template based on the Xeus kernel, see the [`jupyterlite/xeus-python-demo` repository](https://github.com/jupyterlite/xeus-python-demo) +## Rebuilding Pyodide and packages from `pyodide-recipes` + +To rebuild a full Pyodide runtime plus all packages from the latest `pyodide-recipes`: + +1. Ensure you have `conda` and `rustup` (`rustup` must be on `PATH`). +2. From the repo root, run: + ```bash + pyodide/build_world_from_recipes.sh + ``` + This will: + - create or update a `pyodide-env` conda environment based on `pyodide-recipes/environment.yml` + - clone or update `pyodide-recipes` (by default into `_pyodide-recipes/`) + - use `pyodide build-recipes` to build all recipes and generate a `pyodide-lock.json` + - copy the resulting runtime, lock file, and wheels into this repo’s `pyodide/` directory +3. Rebuild the site: + ```bash + ./build.sh + ``` + +Environment variables: + +- `PYODIDE_RECIPES_DIR` – where to clone `pyodide-recipes` (default: `_pyodide-recipes` under the repo root). +- `PYODIDE_ENV_NAME` – conda env name (default: `pyodide-env`). +- `PYODIDE_RECIPES_TARGETS` – package selection string for `pyodide build-recipes` (default: `"*"` for all packages; e.g. `*,!imgui-bundle` to disable a problematic recipe). diff --git a/build.sh b/build.sh index 4edda9d..2176a02 100755 --- a/build.sh +++ b/build.sh @@ -1,12 +1,15 @@ #!/bin/bash -e -python fix_jupyterlite_html.py content +python3 fix_jupyterlite_html.py content cd tskit-launcher/ -jlpm install -jlpm run build -pip install -e . +# Install JS dependencies and build the labextension without relying on jlpm. +npm install + +npx tsc --sourceMap +jupyter labextension build --development True . +pip install -e . cd .. rm -rf dist jupyter lite build --contents content --output-dir dist find content/ -type f -exec cat {} \; | sha256sum | cut -d' ' -f1 > content-hash.txt HASH=$(cat content-hash.txt) -echo "{\"contentHash\":\"$HASH\",\"lastUpdated\":\"$(date -u +%Y-%m-%dT%H:%M:%SZ)\"}" > dist/lab/content-config.json \ No newline at end of file +echo "{\"contentHash\":\"$HASH\",\"lastUpdated\":\"$(date -u +%Y-%m-%dT%H:%M:%SZ)\"}" > dist/lab/content-config.json diff --git a/build_pyodide_world.sh b/build_pyodide_world.sh new file mode 100755 index 0000000..a815b0d --- /dev/null +++ b/build_pyodide_world.sh @@ -0,0 +1,192 @@ +#!/usr/bin/env bash +set -euo pipefail + +# Rebuild a Pyodide runtime + packages from pyodide-recipes, +# limiting the packaged world to the dependency closure of the +# core stack we actually need in the browser. +# +# Usage: +# ./build_pyodide_world.sh +# or override: +# PYODIDE_RECIPES_TARGETS='numpy,scipy,...' ./build_pyodide_world.sh +# +# This script clones/updates pyodide-recipes into _pyodide-recipes/, +# builds recipes into _pyodide-recipes/repodata, copies in the Pyodide +# runtime, then replaces this repo's pyodide/ directory with that output. + +THIS_REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" +TARGET_PYODIDE_DIR="${THIS_REPO_ROOT}/static/pyodide" + +PYODIDE_RECIPES_DIR="${PYODIDE_RECIPES_DIR:-${THIS_REPO_ROOT}/_pyodide-recipes}" +CUSTOM_RECIPES_DIR="${THIS_REPO_ROOT}/pyodide-custom-recipes" +PYODIDE_ENV_NAME="${PYODIDE_ENV_NAME:-pyodide-env}" + +# By default we only ask pyodide-build to build the packages needed for +# the sc2ts / tskit stack: +# - tskit and its dependencies (including msprime and sc2ts) +# - the numerical / plotting stack: numpy, scipy, pandas, matplotlib, bokeh +# - pysam for BAM/CRAM handling +# - numcodecs for tszip's compression backend +# - zarr + tszip + sc2ts + humanize so we can read/write and analyse .tsz files without micropip +# - core Pyodide helpers: micropip, pyodide-http, pyodide-unix-timezones +# +# pyodide-build will compute the full transitive dependency closure of +# these roots. Additional packages (or a full world) can still be built +# by overriding PYODIDE_RECIPES_TARGETS in the environment, e.g.: +# PYODIDE_RECIPES_TARGETS='*' ./build_pyodide_world.sh +PYODIDE_RECIPES_TARGETS="${PYODIDE_RECIPES_TARGETS:-micropip,pyodide-http,pyodide-unix-timezones,tskit,msprime,sc2ts,numpy,scipy,pandas,matplotlib,bokeh,pysam,numcodecs,zarr,humanize,tszip}" + +echo "=== Pyodide world rebuild ===" +echo "Repo root : ${THIS_REPO_ROOT}" +echo "Target pyodide dir : ${TARGET_PYODIDE_DIR}" +echo "pyodide-recipes dir : ${PYODIDE_RECIPES_DIR}" +echo "Conda env name : ${PYODIDE_ENV_NAME}" +echo "Recipe targets : ${PYODIDE_RECIPES_TARGETS}" +echo + +if ! command -v conda >/dev/null 2>&1; then + echo "ERROR: conda is not on PATH. Please install Miniconda/Conda first." >&2 + exit 1 +fi + +if ! command -v rustup >/dev/null 2>&1; then + echo "ERROR: rustup is not on PATH. Install Rust (rustup) first, for example:" >&2 + echo " curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y" >&2 + echo "then restart your shell so that \$HOME/.cargo/bin is on PATH." >&2 + exit 1 +fi + +mkdir -p "${PYODIDE_RECIPES_DIR}" + +if [ ! -d "${PYODIDE_RECIPES_DIR}/.git" ]; then + echo "Cloning pyodide-recipes into ${PYODIDE_RECIPES_DIR} ..." + git clone --recursive https://github.com/pyodide/pyodide-recipes.git "${PYODIDE_RECIPES_DIR}" +else + echo "Updating existing pyodide-recipes clone in ${PYODIDE_RECIPES_DIR} ..." + git -C "${PYODIDE_RECIPES_DIR}" fetch --all --prune + git -C "${PYODIDE_RECIPES_DIR}" checkout main + git -C "${PYODIDE_RECIPES_DIR}" pull --ff-only + git -C "${PYODIDE_RECIPES_DIR}" submodule update --init --recursive +fi + +echo +echo "=== Applying custom recipe overrides (if any) ===" +if [ -d "${CUSTOM_RECIPES_DIR}" ]; then + for pkg_dir in "${CUSTOM_RECIPES_DIR}"/*; do + [ -d "${pkg_dir}" ] || continue + pkg_name="$(basename "${pkg_dir}")" + echo " - Overlaying recipe for ${pkg_name}" + mkdir -p "${PYODIDE_RECIPES_DIR}/packages/${pkg_name}" + cp -a "${pkg_dir}/." "${PYODIDE_RECIPES_DIR}/packages/${pkg_name}/" + done +else + echo " (No custom recipes found in ${CUSTOM_RECIPES_DIR})" +fi + +cd "${PYODIDE_RECIPES_DIR}" + +if [ ! -f environment.yml ]; then + echo "ERROR: environment.yml not found in ${PYODIDE_RECIPES_DIR}" >&2 + exit 1 +fi + +echo +echo "=== Ensuring conda environment ${PYODIDE_ENV_NAME} ===" + +if ! conda env list | awk '{print $1}' | grep -qx "${PYODIDE_ENV_NAME}"; then + echo "Creating conda env ${PYODIDE_ENV_NAME} from environment.yml ..." + conda env create -n "${PYODIDE_ENV_NAME}" -f environment.yml +else + echo "Updating existing conda env ${PYODIDE_ENV_NAME} from environment.yml ..." + conda env update -n "${PYODIDE_ENV_NAME}" -f environment.yml +fi + +echo +echo "=== Activating conda environment ===" +eval "$(conda shell.bash hook)" +conda activate "${PYODIDE_ENV_NAME}" + +echo +echo "=== Installing pyodide-build and cross build environment ===" +python -m pip install ./pyodide-build/ +pyodide xbuildenv install + +echo +echo "=== Installing and configuring Emscripten SDK ===" +python tools/install_and_patch_emscripten.py + +echo +echo "=== Building recipes: ${PYODIDE_RECIPES_TARGETS} ===" +export PIP_CONSTRAINT="$(pwd)/tools/constraints.txt" +export _EMCC_CACHE=1 + +if [ -d emsdk ]; then + # shellcheck disable=SC1091 + source emsdk/emsdk_env.sh +fi + +mkdir -p repodata build-logs + +pyodide build-recipes "${PYODIDE_RECIPES_TARGETS}" --install --install-dir=./repodata --log-dir=build-logs + +echo +echo "=== Copying Pyodide runtime into repodata ===" +./tools/copy_pyodide_runtime.sh ./repodata + +echo +echo "=== Installing new world into ${TARGET_PYODIDE_DIR} ===" +rm -rf "${TARGET_PYODIDE_DIR}" +mkdir -p "${TARGET_PYODIDE_DIR}" +cp -a repodata/. "${TARGET_PYODIDE_DIR}/" + +echo +echo "=== Pruning unused wheels from ${TARGET_PYODIDE_DIR} ===" +PYODIDE_DIR="${TARGET_PYODIDE_DIR}" python - << 'PY' +import json +import os +import sys + +pyodide_dir = os.environ.get("PYODIDE_DIR") +if not pyodide_dir: + raise SystemExit("PYODIDE_DIR is not set") + +lock_path = os.path.join(pyodide_dir, "pyodide-lock.json") +if not os.path.exists(lock_path): + print(f"No pyodide-lock.json in {pyodide_dir}, skipping prune", file=sys.stderr) + raise SystemExit(0) + +with open(lock_path, "r", encoding="utf-8") as f: + data = json.load(f) + +packages = data.get("packages", {}) +keep_names = {pkg.get("file_name") for pkg in packages.values() if pkg.get("file_name")} + +# Always keep the core runtime artifacts and the lock file itself. +keep_names.update( + { + "pyodide.js", + "pyodide.mjs", + "pyodide.asm.js", + "pyodide.asm.wasm", + "python_stdlib.zip", + "pyodide-lock.json", + } +) + +removed = 0 +for entry in os.listdir(pyodide_dir): + if entry in keep_names: + continue + path = os.path.join(pyodide_dir, entry) + if os.path.isfile(path): + os.remove(path) + removed += 1 + +print(f"Pruned {removed} unused files from {pyodide_dir}") +PY + +echo +echo "Done. The pyodide/ directory now holds the rebuilt world." +echo "Rebuild the site with:" +echo " cd \"${THIS_REPO_ROOT}\"" +echo " ./build.sh" diff --git a/clean.sh b/clean.sh new file mode 100755 index 0000000..672b719 --- /dev/null +++ b/clean.sh @@ -0,0 +1,54 @@ +#!/usr/bin/env bash +set -euo pipefail + +# Remove large, reproducible build artifacts so that a fresh, +# trimmed Pyodide world and JupyterLite site can be generated. + +ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" + +echo "Cleaning build artifacts under ${ROOT_DIR}" + +# JupyterLite build output +if [ -d "${ROOT_DIR}/dist" ]; then + echo " - Removing dist/" + rm -rf "${ROOT_DIR}/dist" +fi + +# Pyodide runtime + wheels copied from pyodide-recipes +if [ -d "${ROOT_DIR}/pyodide" ]; then + echo " - Removing legacy pyodide/ (root-level)" + rm -rf "${ROOT_DIR}/pyodide" +fi + +if [ -d "${ROOT_DIR}/static/pyodide" ]; then + echo " - Removing static/pyodide/" + rm -rf "${ROOT_DIR}/static/pyodide" +fi + +# pyodide-recipes local build outputs (can always be regenerated) +if [ -d "${ROOT_DIR}/_pyodide-recipes/repodata" ]; then + echo " - Removing _pyodide-recipes/repodata/ (best effort)" + rm -rf "${ROOT_DIR}/_pyodide-recipes/repodata" || echo " (could not remove repodata; check permissions)" +fi + +if [ -d "${ROOT_DIR}/_pyodide-recipes/build-logs" ]; then + echo " - Removing _pyodide-recipes/build-logs/ (best effort)" + rm -rf "${ROOT_DIR}/_pyodide-recipes/build-logs" || echo " (could not remove build-logs; check permissions)" +fi + +# Any locally built Pyodide wheels sitting at the repo root (e.g. tskit) +TSKIT_WHEEL_PATTERN="${ROOT_DIR}/tskit-"*"pyodide_2025_0_wasm32.whl" +shopt -s nullglob +TSKIT_WHEELS=( ${TSKIT_WHEEL_PATTERN} ) +shopt -u nullglob +if [ "${#TSKIT_WHEELS[@]}" -gt 0 ]; then + echo " - Removing local Pyodide tskit wheels:" + for w in "${TSKIT_WHEELS[@]}"; do + echo " * ${w##${ROOT_DIR}/}" + rm -f "${w}" + done +fi + +echo "Done. You can now run:" +echo " ./build_pyodide_world.sh" +echo " ./build.sh" diff --git a/content-hash.txt b/content-hash.txt index 7ce4e8b..5501ad6 100644 --- a/content-hash.txt +++ b/content-hash.txt @@ -1 +1 @@ -653300a10ae14d157f9337dff588e992e6904627b13c4f5352e6ab3cd538079e +f468ef7ef8a11d8922fde09b94ef1e2748f8b5a3f80adac729665ca28aa93d2c diff --git a/content/sc2ts.ipynb b/content/sc2ts.ipynb index 6ebf3e4..6710bb7 100644 --- a/content/sc2ts.ipynb +++ b/content/sc2ts.ipynb @@ -1,53 +1,1543 @@ { "cells": [ + { + "cell_type": "markdown", + "id": "3a0276fe-b7cc-4dbd-aecb-d8aff506014c", + "metadata": {}, + "source": [ + "# Analysing the sc2ts ARG using tskit, numpy and pandas\n", + "\n", + "This notebooks shows examples of analysing the 2.48 million sample sc2ts ARG using the [tskit Python API](https://tskit.dev/tskit/docs/), in conjuction with Pandas and with an emphasis on using vectorised approaches with Numpy. This is to showcase the ease and efficiency with which pandemic scale analyses can be done directly within a notebook environment using only Python, and to provide a starting point for further analyses. We focus on the core computational tasks one might like to perform on a pandemic scale ARG, with the minimal set of external dependencies required to do this.\n", + "\n", + "Please see the tskit [documentation](https://tskit.dev/tskit/docs/stable/) for detailed information on the Python APIs, and the [tskit tutorials](https://tskit.dev/tutorials/intro.html) site for an introduction to tskit and help with various tasks such as visualisation. Please see the [preprint](https://www.biorxiv.org/content/10.1101/2023.06.08.544212) for background and further details on all aspects of sc2ts and the ARG." + ] + }, { "cell_type": "code", - "execution_count": null, - "id": "import-setup", + "execution_count": 1, + "id": "d3d287ba-0c5d-4d87-a1ab-d0da965bddae", "metadata": {}, "outputs": [], "source": [ - "import micropip\n", - "await micropip.install(\"tszip\")\n", "import tszip\n", - "import tskit" + "import sc2ts\n", + "import numpy as np" + ] + }, + { + "cell_type": "markdown", + "id": "47974ad3-8126-4b8c-ab44-2e3b7098f047", + "metadata": {}, + "source": [ + "First, we load the ARG into memory from the compressed representation using [tszip](https://tskit.dev/software/tszip.html), which typically takes less than a second. The object we get back is a [tskit TreeSequence](https://tskit.dev/tskit/docs/stable/python-api.html#tskit.TreeSequence), which we call ``ts`` by convention." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "feab8489-6ae9-4ab7-ab78-25f9fb7a152e", + "metadata": {}, + "outputs": [], + "source": [ +"ts = tszip.load(\"data/sc2ts_viridian_v1.2.trees.tsz\")" + ] + }, + { + "cell_type": "markdown", + "id": "a5913e59-6cf3-4f4f-9323-672ffc118abc", + "metadata": {}, + "source": [ + "When viewed in a notebook environment, the TreeSequence gives some summary information about its contents:" ] }, { "cell_type": "code", - "execution_count": null, - "id": "load-tsz", + "execution_count": 3, + "id": "199f6b55-c50d-49b3-baec-d884fc17ca46", "metadata": {}, "outputs": [ { "data": { - "text/html": "\n
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Provenance TimestampSoftware NameVersionCommandFull record
11 September, 2025 at 09:02:43 PMsc2ts0.0.4.dev716+g109ed6a6aminimise_metadata\n
\n Details\n \n
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\n dict\n schema_version: 1.0.0
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\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev716+g109ed6a6a
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\n dict\n command: minimise_metadata
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pango: pango
scorpio: scorpio
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node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
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version: 3.12.11
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user_time: 282.34
sys_time: 3.31
max_memory: 8572321792
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11 September, 2025 at 08:57:47 PMtsdate0.2.3variational_gamma\n
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\n dict\n schema_version: 1.0.0
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\n dict\n name: tsdate
version: 0.2.3
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recombination_rate: None
time_units: days
progress: False
population_size: None
eps: 1e-10
max_iterations: 25
max_shape: 1000
rescaling_intervals: 0
rescaling_iterations: 5
match_segregating_sites: False
regularise_roots: True
singletons_phased: True
command: variational_gamma
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\n dict\n system: Linux
node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
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\n dict\n implementation: CPython
version: 3.12.11
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11 September, 2025 at 08:27:51 PMUnknownUnknownUnknown\n
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\n dict\n command: scripts/run_nonsample_dating.p
y
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\n list\n sc2ts_v1_2023-02-
21_pr_pp_mp_aph_bps_pango.tree
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11 September, 2025 at 12:40:10 PMsc2ts0.0.4.dev716+g109ed6a6aapply_node_parsimony_heuristics\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
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\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev716+g109ed6a6a
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\n dict\n command: apply_node_parsimony_heuristic
s
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\n dict\n system: Linux
node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
\n
\n
\n
\n
\n python:\n
\n dict\n implementation: CPython
version: 3.12.11
\n
\n
\n
\n
\n libraries:\n
\n dict\n \n
\n kastore:\n
\n dict\n version: 2.1.1
\n
\n
\n
\n
\n tskit:\n
\n dict\n version: 0.6.4
\n
\n
\n
\n
\n tsinfer:\n
\n dict\n version: 0.1.dev1455+g7522bcc8d
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n resources:\n
\n dict\n elapsed_time: 1725.9827859401703
user_time: 1691.29
sys_time: 37.32
max_memory: 14721216512
\n
\n
\n
\n
\n
\n \n
\n
11 September, 2025 at 11:38:48 AMsc2ts0.0.4.dev716+g109ed6a6amap_parsimony\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev716+g109ed6a6a
\n
\n
\n
\n
\n parameters:\n
\n dict\n command: map_parsimony
dataset: ../data/viridian_mafft_2024-
10-14_v1.vcz.zip
\n
\n sites:\n
\n list\n 203
222
335
337
683
686
687
688
689
690
691
692
693
694
823
1191
1684
1820
1912
3096
4579
5284
5512
5812
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6514
6515
7528
9430
... and 133 more\n
\n
\n
\n
\n
\n
\n
\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
\n
\n
\n
\n
\n python:\n
\n dict\n implementation: CPython
version: 3.12.11
\n
\n
\n
\n
\n libraries:\n
\n dict\n \n
\n kastore:\n
\n dict\n version: 2.1.1
\n
\n
\n
\n
\n tskit:\n
\n dict\n version: 0.6.4
\n
\n
\n
\n
\n tsinfer:\n
\n dict\n version: 0.1.dev1455+g7522bcc8d
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n resources:\n
\n dict\n elapsed_time: 113.88616251945496
user_time: 113.53999999999999
sys_time: 15.16
max_memory: 9682702336
\n
\n
\n
\n
\n
\n \n
\n
11 September, 2025 at 11:33:56 AMsc2ts0.0.4.dev716+g109ed6a6apush_up_unary_recombinant_mutations\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev716+g109ed6a6a
\n
\n
\n
\n
\n parameters:\n
\n dict\n command: push_up_unary_recombinant_muta
tions
\n
\n
\n
\n
\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
\n
\n
\n
\n
\n python:\n
\n dict\n implementation: CPython
version: 3.12.11
\n
\n
\n
\n
\n libraries:\n
\n dict\n \n
\n kastore:\n
\n dict\n version: 2.1.1
\n
\n
\n
\n
\n tskit:\n
\n dict\n version: 0.6.4
\n
\n
\n
\n
\n tsinfer:\n
\n dict\n version: 0.1.dev1455+g7522bcc8d
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n resources:\n
\n dict\n elapsed_time: 2.014835834503174
user_time: 1222.18
sys_time: 19.299999999999997
max_memory: 9223966720
\n
\n
\n
\n
\n
\n \n
\n
11 September, 2025 at 11:33:50 AMsc2ts0.0.4.dev716+g109ed6a6aappend_exact_matches\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev716+g109ed6a6a
\n
\n
\n
\n
\n parameters:\n
\n dict\n command: append_exact_matches
match_db: ../inference/results/v1-
beta1.matches.db
\n
\n
\n
\n
\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
\n
\n
\n
\n
\n python:\n
\n dict\n implementation: CPython
version: 3.12.11
\n
\n
\n
\n
\n libraries:\n
\n dict\n \n
\n kastore:\n
\n dict\n version: 2.1.1
\n
\n
\n
\n
\n tskit:\n
\n dict\n version: 0.6.4
\n
\n
\n
\n
\n tsinfer:\n
\n dict\n version: 0.1.dev1455+g7522bcc8d
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n resources:\n
\n dict\n elapsed_time: 1241.5077295303345
user_time: 1218.72
sys_time: 17.549999999999997
max_memory: 6132613120
\n
\n
\n
\n
\n
\n \n
\n
20 August, 2025 at 09:18:38 AMsc2ts0.0.4.dev712+gb7a68b468push_up_unary_recombinant_mutations\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev712+gb7a68b468
\n
\n
\n
\n
\n parameters:\n
\n dict\n command: push_up_unary_recombinant_muta
tions
\n
\n
\n
\n
\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
\n
\n
\n
\n
\n python:\n
\n dict\n implementation: CPython
version: 3.12.11
\n
\n
\n
\n
\n libraries:\n
\n dict\n \n
\n kastore:\n
\n dict\n version: 2.1.1
\n
\n
\n
\n
\n tskit:\n
\n dict\n version: 0.6.4
\n
\n
\n
\n
\n tsinfer:\n
\n dict\n version: 0.1.dev1455+g7522bcc8d
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n resources:\n
\n dict\n elapsed_time: 1.3764989376068115
user_time: 3.36
sys_time: 1.7
max_memory: 4453330944
\n
\n
\n
\n
\n
\n \n
\n
19 January, 2025 at 04:26:26 AMsc2ts0.0.4.dev536+g33a72d6extend\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev536+g33a72d6
\n
\n
\n
\n
\n parameters:\n
\n dict\n command: extend
dataset: /tmp/jk/viridian_2024-04-
29.alpha1.zarr.zip
date: 2023-02-21
base_ts: results/v1-beta1/v1-
beta1_2023-02-20.ts
match_db: /tmp/jk/matches/v1-
beta1.matches.db
date_field: Date_tree
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ERR5469699
ERR5469807
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ERR5701881
ERR5690052
ERR5690920
SRR17041376
SRR17461792
\n
\n
\n
num_mismatches: 4
hmm_cost_threshold: 7
min_group_size: 10
min_root_mutations: 2
min_different_dates: 3
max_mutations_per_sample: 5
max_recurrent_mutations: 2
deletions_as_missing: True
max_daily_samples: None
show_progress: True
retrospective_window: 7
max_missing_sites: 500
random_seed: 42
num_threads: 80
memory_limit: 250
\n
\n
\n
\n
\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: epyc000.hpc.in.bmrc.ox.ac.uk
release: 4.18.0-553.16.1.el8_10.x86_64
version: #1 SMP Thu Aug 8 17:47:08 UTC
2024
machine: x86_64
\n
\n
\n
\n
\n python:\n
\n dict\n implementation: CPython
version: 3.11.3
\n
\n
\n
\n
\n libraries:\n
\n dict\n \n
\n kastore:\n
\n dict\n version: 2.1.1
\n
\n
\n
\n
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\n
\n
\n
\n
\n tsinfer:\n
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\n
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n resources:\n
\n dict\n elapsed_time: 23.96233034133911
user_time: 20.23
sys_time: 3.54
max_memory: 14884753408
\n
\n
\n
\n
\n
\n \n
\n
19 January, 2025 at 04:26:00 AMsc2ts0.0.4.dev536+g33a72d6extend\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev536+g33a72d6
\n
\n
\n
\n
\n parameters:\n
\n dict\n command: extend
dataset: /tmp/jk/viridian_2024-04-
29.alpha1.zarr.zip
date: 2023-02-20
base_ts: results/v1-beta1/v1-
beta1_2023-02-19.ts
match_db: /tmp/jk/matches/v1-
beta1.matches.db
date_field: Date_tree
\n
\n include_samples:\n
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ERR5521603
ERR5531143
ERR5532096
ERR5532118
ERR5537492
ERR5676810
ERR5690893
ERR5690055
ERR5690921
ERR5695631
ERR5701881
ERR5690052
ERR5690920
SRR17041376
SRR17461792
\n
\n
\n
num_mismatches: 4
hmm_cost_threshold: 7
min_group_size: 10
min_root_mutations: 2
min_different_dates: 3
max_mutations_per_sample: 5
max_recurrent_mutations: 2
deletions_as_missing: True
max_daily_samples: None
show_progress: True
retrospective_window: 7
max_missing_sites: 500
random_seed: 42
num_threads: 80
memory_limit: 250
\n
\n
\n
\n
\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: epyc000.hpc.in.bmrc.ox.ac.uk
release: 4.18.0-553.16.1.el8_10.x86_64
version: #1 SMP Thu Aug 8 17:47:08 UTC
2024
machine: x86_64
\n
\n
\n
\n
\n python:\n
\n dict\n implementation: CPython
version: 3.11.3
\n
\n
\n
\n
\n libraries:\n
\n dict\n \n
\n kastore:\n
\n dict\n version: 2.1.1
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\n
\n
\n
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\n
\n
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\n
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n resources:\n
\n dict\n elapsed_time: 241.07852435112
user_time: 1551.5
sys_time: 15.07
max_memory: 34759606272
\n
\n
\n
\n
\n
\n \n
\n
... 1125 more
\n
\n
\n
\n ", + "text/html": "\n
\n \n
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\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
\n \n Tree Sequence \n
Trees316
Sequence Length29 904
Time Unitsdays
Sample Nodes2 482 157
Total Size408.1 MiB
Metadata\n
\n \n
\n dict\n time_zero_date: 2023-02-21
\n
\n
\n
\n
\n
\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
TableRowsSizeHas Metadata
Edges2 748 83883.9 MiB\n \n
Individuals024 Bytes\n \n
Migrations08 Bytes\n \n
Mutations2 285 34480.6 MiB\n \n
Nodes2 747 985220.1 MiB\n ✅\n
Populations08 Bytes\n \n
Provenances1 1351.7 MiB\n \n
Sites29 893729.8 KiB\n \n
\n
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\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
Provenance TimestampSoftware NameVersionCommandFull record
11 September, 2025 at 09:02:43 PMsc2ts0.0.4.dev716+g109ed6a6aminimise_metadata\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev716+g109ed6a6a
\n
\n
\n
\n
\n parameters:\n
\n dict\n command: minimise_metadata
\n
\n field_mapping:\n
\n dict\n strain: sample_id
pango: pango
scorpio: scorpio
\n
\n
\n
\n
\n
\n
\n
\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
\n
\n
\n
\n
\n python:\n
\n dict\n implementation: CPython
version: 3.12.11
\n
\n
\n
\n
\n libraries:\n
\n dict\n \n
\n kastore:\n
\n dict\n version: 2.1.1
\n
\n
\n
\n
\n tskit:\n
\n dict\n version: 0.6.4
\n
\n
\n
\n
\n tsinfer:\n
\n dict\n version: 0.1.dev1455+g7522bcc8d
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n resources:\n
\n dict\n elapsed_time: 281.8967273235321
user_time: 282.34
sys_time: 3.31
max_memory: 8572321792
\n
\n
\n
\n
\n
\n \n
\n
11 September, 2025 at 08:57:47 PMtsdate0.2.3variational_gamma\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: tsdate
version: 0.2.3
\n
\n
\n
\n
\n parameters:\n
\n dict\n mutation_rate: 9.967653503392e-07
recombination_rate: None
time_units: days
progress: False
population_size: None
eps: 1e-10
max_iterations: 25
max_shape: 1000
rescaling_intervals: 0
rescaling_iterations: 5
match_segregating_sites: False
regularise_roots: True
singletons_phased: True
command: variational_gamma
\n
\n
\n
\n
\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
\n
\n
\n
\n
\n python:\n
\n dict\n implementation: CPython
version: 3.12.11
\n
\n
\n
\n
\n libraries:\n
\n dict\n \n
\n tskit:\n
\n dict\n version: 0.6.4
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n resources:\n
\n dict\n elapsed_time: 1786.5585663318634
user_time: 1477.3799999999999
sys_time: 365.09999999999997
max_memory: 14737055744
\n
\n
\n
\n
\n
\n \n
\n
11 September, 2025 at 08:27:51 PMUnknownUnknownUnknown\n
\n Details\n \n
\n \n
\n dict\n command: scripts/run_nonsample_dating.p
y
\n
\n args:\n
\n list\n sc2ts_v1_2023-02-
21_pr_pp_mp_aph_bps_pango.tree
s
sc2ts_v1_2023-02-
21_pr_pp_mp_aph_bps_pango_date
d.trees
\n
\n
\n
\n
\n
\n \n
\n
11 September, 2025 at 12:40:10 PMsc2ts0.0.4.dev716+g109ed6a6aapply_node_parsimony_heuristics\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev716+g109ed6a6a
\n
\n
\n
\n
\n parameters:\n
\n dict\n command: apply_node_parsimony_heuristic
s
\n
\n
\n
\n
\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
\n
\n
\n
\n
\n python:\n
\n dict\n implementation: CPython
version: 3.12.11
\n
\n
\n
\n
\n libraries:\n
\n dict\n \n
\n kastore:\n
\n dict\n version: 2.1.1
\n
\n
\n
\n
\n tskit:\n
\n dict\n version: 0.6.4
\n
\n
\n
\n
\n tsinfer:\n
\n dict\n version: 0.1.dev1455+g7522bcc8d
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n resources:\n
\n dict\n elapsed_time: 1725.9827859401703
user_time: 1691.29
sys_time: 37.32
max_memory: 14721216512
\n
\n
\n
\n
\n
\n \n
\n
11 September, 2025 at 11:38:48 AMsc2ts0.0.4.dev716+g109ed6a6amap_parsimony\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev716+g109ed6a6a
\n
\n
\n
\n
\n parameters:\n
\n dict\n command: map_parsimony
dataset: ../data/viridian_mafft_2024-
10-14_v1.vcz.zip
\n
\n sites:\n
\n list\n 203
222
335
337
683
686
687
688
689
690
691
692
693
694
823
1191
1684
1820
1912
3096
4579
5284
5512
5812
5869
6513
6514
6515
7528
9430
... and 133 more\n
\n
\n
\n
\n
\n
\n
\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
\n
\n
\n
\n
\n python:\n
\n dict\n implementation: CPython
version: 3.12.11
\n
\n
\n
\n
\n libraries:\n
\n dict\n \n
\n kastore:\n
\n dict\n version: 2.1.1
\n
\n
\n
\n
\n tskit:\n
\n dict\n version: 0.6.4
\n
\n
\n
\n
\n tsinfer:\n
\n dict\n version: 0.1.dev1455+g7522bcc8d
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n
\n resources:\n
\n dict\n elapsed_time: 113.88616251945496
user_time: 113.53999999999999
sys_time: 15.16
max_memory: 9682702336
\n
\n
\n
\n
\n
\n \n
\n
11 September, 2025 at 11:33:56 AMsc2ts0.0.4.dev716+g109ed6a6apush_up_unary_recombinant_mutations\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev716+g109ed6a6a
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\n dict\n command: push_up_unary_recombinant_muta
tions
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\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
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\n python:\n
\n dict\n implementation: CPython
version: 3.12.11
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user_time: 1222.18
sys_time: 19.299999999999997
max_memory: 9223966720
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11 September, 2025 at 11:33:50 AMsc2ts0.0.4.dev716+g109ed6a6aappend_exact_matches\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
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\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev716+g109ed6a6a
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\n parameters:\n
\n dict\n command: append_exact_matches
match_db: ../inference/results/v1-
beta1.matches.db
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\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
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version: 3.12.11
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max_memory: 6132613120
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20 August, 2025 at 09:18:38 AMsc2ts0.0.4.dev712+gb7a68b468push_up_unary_recombinant_mutations\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
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\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev712+gb7a68b468
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\n dict\n command: push_up_unary_recombinant_muta
tions
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\n dict\n \n
\n os:\n
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node: holly
release: 5.10.0-24-amd64
version: #1 SMP Debian 5.10.179-5
(2023-08-08)
machine: x86_64
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version: 3.12.11
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user_time: 3.36
sys_time: 1.7
max_memory: 4453330944
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19 January, 2025 at 04:26:26 AMsc2ts0.0.4.dev536+g33a72d6extend\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev536+g33a72d6
\n
\n
\n
\n
\n parameters:\n
\n dict\n command: extend
dataset: /tmp/jk/viridian_2024-04-
29.alpha1.zarr.zip
date: 2023-02-21
base_ts: results/v1-beta1/v1-
beta1_2023-02-20.ts
match_db: /tmp/jk/matches/v1-
beta1.matches.db
date_field: Date_tree
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\n
\n
num_mismatches: 4
hmm_cost_threshold: 7
min_group_size: 10
min_root_mutations: 2
min_different_dates: 3
max_mutations_per_sample: 5
max_recurrent_mutations: 2
deletions_as_missing: True
max_daily_samples: None
show_progress: True
retrospective_window: 7
max_missing_sites: 500
random_seed: 42
num_threads: 80
memory_limit: 250
\n
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\n
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\n environment:\n
\n dict\n \n
\n os:\n
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node: epyc000.hpc.in.bmrc.ox.ac.uk
release: 4.18.0-553.16.1.el8_10.x86_64
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2024
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user_time: 20.23
sys_time: 3.54
max_memory: 14884753408
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\n
\n \n
\n
19 January, 2025 at 04:26:00 AMsc2ts0.0.4.dev536+g33a72d6extend\n
\n Details\n \n
\n \n
\n dict\n schema_version: 1.0.0
\n
\n software:\n
\n dict\n name: sc2ts
version: 0.0.4.dev536+g33a72d6
\n
\n
\n
\n
\n parameters:\n
\n dict\n command: extend
dataset: /tmp/jk/viridian_2024-04-
29.alpha1.zarr.zip
date: 2023-02-20
base_ts: results/v1-beta1/v1-
beta1_2023-02-19.ts
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\n
num_mismatches: 4
hmm_cost_threshold: 7
min_group_size: 10
min_root_mutations: 2
min_different_dates: 3
max_mutations_per_sample: 5
max_recurrent_mutations: 2
deletions_as_missing: True
max_daily_samples: None
show_progress: True
retrospective_window: 7
max_missing_sites: 500
random_seed: 42
num_threads: 80
memory_limit: 250
\n
\n
\n
\n
\n environment:\n
\n dict\n \n
\n os:\n
\n dict\n system: Linux
node: epyc000.hpc.in.bmrc.ox.ac.uk
release: 4.18.0-553.16.1.el8_10.x86_64
version: #1 SMP Thu Aug 8 17:47:08 UTC
2024
machine: x86_64
\n
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\n
\n python:\n
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version: 3.11.3
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max_memory: 34759606272
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\n
\n
\n
\n
\n \n
\n
... 1125 more
\n
\n
\n
\n To cite this software, please consult the citation manual: https://tskit.dev/citation/\n
\n
\n ", "text/plain": [ - "" + "" ] }, - "execution_count": 4, + "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "ts = tszip.load(\"data/sc2ts_viridian_v1.2.trees.tsz\")\n", "ts" ] }, + { + "cell_type": "markdown", + "id": "dc445355-65ab-43e3-b9d3-370f5a0b6d94", + "metadata": {}, + "source": [ + "## Information on nodes\n", + "\n", + "The [sc2ts Python API](https://tskit.dev/sc2ts/docs/stable/api.html) provides a few utility functions that take advantage of specific structure of the sc2ts ARG and its metadata. The ``node_data`` function returns a Pandas Dataframe summarising the nodes in the ARG, and in particular, makes the key ``sample_id``, ``pango`` and ``scorpio`` metadata fields efficiently accessible." + ] + }, { "cell_type": "code", - "execution_count": null, - "id": "d564dce2", + "execution_count": 4, + "id": "5c77c97e-9595-4620-ab1d-246df23cf7a5", "metadata": {}, - "outputs": [], - "source": [] + "outputs": [ + { + "data": { + "text/html": "
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pangosample_idscorpionode_idis_sampleis_recombinantnum_mutationsdate
0BVestigial_ignore.0FalseFalse02019-11-23
1BWuhan/Hu-1/2019.1FalseFalse02019-12-26
2ASRR11772659.2TrueFalse12020-01-19
3BSRR11397727.3TrueFalse02020-01-24
4BSRR11397730.4TrueFalse02020-01-24
...........................
2747980BA.2.1Omicron (BA.2-like)2747980FalseFalse12022-01-03
2747981CH.1.1Omicron (BA.2-like)2747981FalseFalse12022-09-28
2747982BA.5.1Omicron (BA.5-like)2747982FalseFalse22022-05-31
2747983BU.1Omicron (BA.5-like)2747983FalseFalse42022-06-13
2747984AY.44Delta (B.1.617.2-like)2747984FalseFalse22021-06-15
\n

2747985 rows × 8 columns

\n
", + "text/plain": [ + " pango sample_id scorpio node_id is_sample \\\n", + "0 B Vestigial_ignore . 0 False \n", + "1 B Wuhan/Hu-1/2019 . 1 False \n", + "2 A SRR11772659 . 2 True \n", + "3 B SRR11397727 . 3 True \n", + "4 B SRR11397730 . 4 True \n", + "... ... ... ... ... ... \n", + "2747980 BA.2.1 Omicron (BA.2-like) 2747980 False \n", + "2747981 CH.1.1 Omicron (BA.2-like) 2747981 False \n", + "2747982 BA.5.1 Omicron (BA.5-like) 2747982 False \n", + "2747983 BU.1 Omicron (BA.5-like) 2747983 False \n", + "2747984 AY.44 Delta (B.1.617.2-like) 2747984 False \n", + "\n", + " is_recombinant num_mutations date \n", + "0 False 0 2019-11-23 \n", + "1 False 0 2019-12-26 \n", + "2 False 1 2020-01-19 \n", + "3 False 0 2020-01-24 \n", + "4 False 0 2020-01-24 \n", + "... ... ... ... \n", + "2747980 False 1 2022-01-03 \n", + "2747981 False 1 2022-09-28 \n", + "2747982 False 2 2022-05-31 \n", + "2747983 False 4 2022-06-13 \n", + "2747984 False 2 2021-06-15 \n", + "\n", + "[2747985 rows x 8 columns]" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dfn = sc2ts.node_data(ts)\n", + "dfn" + ] + }, + { + "cell_type": "markdown", + "id": "34b33ff1-e17a-42a7-ad14-0595b7e37b16", + "metadata": {}, + "source": [ + "Pandas provides many powerful functions. For example, here is a breakdown of the numbers of nodes by their Scorpio assignment:" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "810c0426-a471-4e6f-8c80-798769bd0b45", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "data": { + "text/plain": [ + "scorpio\n", + "Delta (B.1.617.2-like) 583392\n", + "Delta (AY.4-like) 554731\n", + "Omicron (BA.1-like) 371937\n", + "Omicron (BA.2-like) 366040\n", + "Alpha (B.1.1.7-like) 317036\n", + "Omicron (BA.5-like) 194121\n", + ". 192203\n", + "Delta (AY.4.2-like) 92668\n", + "Omicron (BA.4-like) 27625\n", + "Iota (B.1.526-like) 11026\n", + "Epsilon (B.1.429-like) 8526\n", + "Omicron (XBB.1.5-like) 6020\n", + "Gamma (P.1-like) 5008\n", + "Epsilon (B.1.427-like) 4522\n", + "Beta (B.1.351-like) 3027\n", + "Mu (B.1.621-like) 1484\n", + "Delta (B.1.617.2-like) +K417N 1424\n", + "Omicron (XE-like) 1177\n", + "B.1.1.318-like 1118\n", + "Omicron (XBB.1-like) 1037\n", + "Eta (B.1.525-like) 893\n", + "Omicron (XBB-like) 785\n", + "B.1.617.1-like 495\n", + "Omicron (Unassigned) 357\n", + "Zeta (P.2-like) 355\n", + "B.1.1.7-like+E484K 319\n", + "Lambda (C.37-like) 233\n", + "A.23.1-like 191\n", + "AV.1-like 149\n", + "A.23.1-like+E484K 50\n", + "Probable Omicron (Unassigned) 36\n", + "Name: count, dtype: Int64" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dfn[\"scorpio\"].value_counts()" + ] + }, + { + "cell_type": "markdown", + "id": "de63548c-83e5-467d-9188-baaab10add91", + "metadata": {}, + "source": [ + "We can then use this to identify specific nodes. Suppose we wanted to find the first Alpha node. To do this, we simply need to find oldest node with the corresponding Pango label.\n", + "\n", + "**NOTE** The dataframe returned by ``node_data`` has a ``date`` field, which gives the estimated date for each node, which has day-precision. In order to find the oldest node reliably we need finer precision, which is provided by the ``time`` column in the tskit \n", + "[node table](https://tskit.dev/tskit/docs/stable/data-model.html#node-table). To access this information in Pandas, we add this field to the dataframe. Then, we sort the rows by time and then extract the first record for each Pango designation:" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "aa76a310-d128-4874-8749-c70a255ffc13", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "data": { + "text/html": "
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sample_idscorpionode_idis_sampleis_recombinantnum_mutationsdatetime
pango
A.9FalseFalse22019-12-261153.000000
A.1.227FalseFalse22020-01-191129.000000
A.2.530FalseFalse42020-02-011116.000000
A.2.2.1190FalseFalse12020-02-261091.109256
A.2.3.1186FalseFalse22020-02-211096.465780
...........................
XWOmicron (BA.2-like)1159411FalseTrue12022-03-10348.300416
XYOmicron (Unassigned)1187989FalseTrue22022-03-16342.625280
XZOmicron (BA.2-like)1163537FalseFalse12022-03-05353.377858
Y.1.55861FalseFalse12020-08-18917.000000
Z.1ERR4664951.30483TrueFalse32020-09-15889.000000
\n

2058 rows × 8 columns

\n
", + "text/plain": [ + " sample_id scorpio node_id is_sample is_recombinant \\\n", + "pango \n", + "A . 9 False False \n", + "A.1 . 227 False False \n", + "A.2 . 530 False False \n", + "A.2.2 . 1190 False False \n", + "A.2.3 . 1186 False False \n", + "... ... ... ... ... ... \n", + "XW Omicron (BA.2-like) 1159411 False True \n", + "XY Omicron (Unassigned) 1187989 False True \n", + "XZ Omicron (BA.2-like) 1163537 False False \n", + "Y.1 . 55861 False False \n", + "Z.1 ERR4664951 . 30483 True False \n", + "\n", + " num_mutations date time \n", + "pango \n", + "A 2 2019-12-26 1153.000000 \n", + "A.1 2 2020-01-19 1129.000000 \n", + "A.2 4 2020-02-01 1116.000000 \n", + "A.2.2 1 2020-02-26 1091.109256 \n", + "A.2.3 2 2020-02-21 1096.465780 \n", + "... ... ... ... \n", + "XW 1 2022-03-10 348.300416 \n", + "XY 2 2022-03-16 342.625280 \n", + "XZ 1 2022-03-05 353.377858 \n", + "Y.1 1 2020-08-18 917.000000 \n", + "Z.1 3 2020-09-15 889.000000 \n", + "\n", + "[2058 rows x 8 columns]" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dfn[\"time\"] = ts.nodes_time\n", + "dfn_pango = dfn.sort_values(\"time\", ascending=False).groupby([\"pango\"]).first()\n", + "dfn_pango" + ] + }, + { + "cell_type": "markdown", + "id": "b4b2c94f-ba73-4fd2-ab7e-7b772fc9d731", + "metadata": {}, + "source": [ + "We can then extract the \"alpha origin\" node easily:" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "5bc6d76b-f437-4545-aaba-b1f760c44275", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "sample_id \n", + "scorpio Alpha (B.1.1.7-like)\n", + "node_id 86456\n", + "is_sample False\n", + "is_recombinant False\n", + "num_mutations 36\n", + "date 2020-09-23 00:00:00\n", + "time 881.613313\n", + "Name: B.1.1.7, dtype: object" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "alpha_origin = dfn_pango.loc[\"B.1.1.7\"]\n", + "alpha_origin" + ] + }, + { + "cell_type": "markdown", + "id": "7175a223-9ab3-429d-b846-1462dceae201", + "metadata": {}, + "source": [ + "## Information on mutations\n", + "\n", + "The sc2ts Python API also provides a way to extract information about mutations. " + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "86805960-1b06-4962-8872-64a77e60dd1d", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": "
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mutation_idsite_idpositionparentinherited_statederived_statedate
node
64428002425-1TA2021-09-20
1291513738-1AG2020-04-21
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........................
69182122853392983929850-1AG2021-10-18
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111250722853432983929850-1AG2022-02-04
\n

2285344 rows × 7 columns

\n
", + "text/plain": [ + " mutation_id site_id position parent inherited_state derived_state \\\n", + "node \n", + "644280 0 24 25 -1 T A \n", + "12915 1 37 38 -1 A G \n", + "344292 2 42 43 -1 T A \n", + "427855 3 42 43 -1 T C \n", + "670767 4 42 43 -1 T C \n", + "... ... ... ... ... ... ... \n", + "691821 2285339 29839 29850 -1 A G \n", + "719257 2285340 29839 29850 -1 A G \n", + "952268 2285341 29839 29850 -1 A G \n", + "1129360 2285342 29839 29850 -1 A G \n", + "1112507 2285343 29839 29850 -1 A G \n", + "\n", + " date \n", + "node \n", + "644280 2021-09-20 \n", + "12915 2020-04-21 \n", + "344292 2021-07-17 \n", + "427855 2021-07-25 \n", + "670767 2021-08-21 \n", + "... ... \n", + "691821 2021-10-18 \n", + "719257 2021-10-21 \n", + "952268 2021-12-13 \n", + "1129360 2022-01-08 \n", + "1112507 2022-02-04 \n", + "\n", + "[2285344 rows x 7 columns]" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dfm = sc2ts.mutation_data(ts).set_index(\"node\")\n", + "dfm" + ] + }, + { + "cell_type": "markdown", + "id": "3244f7ee-3818-46a5-967e-fcb162c8d08e", + "metadata": {}, + "source": [ + "This dataframe has information about each mutation, including the genome position (``position``) and node over which the mutation occured. Here, we're interested in finding all the mutations immediately ancestral to the Alpha origin node found above, and so we add an index on the ``node`` field. Then, getting the mutations is quick and easy:" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "c5fbc217-c3bf-4d64-9cb2-fc47a4468179", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": "
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mutation_idsite_idpositionparentinherited_statederived_statedate
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\n
", + "text/plain": [ + " mutation_id site_id position parent inherited_state derived_state \\\n", + "node \n", + "86456 160960 910 913 -1 C T \n", + "86456 472353 5385 5388 -1 C A \n", + "86456 507747 5983 5986 -1 C T \n", + "86456 575045 6951 6954 -1 T C \n", + "86456 812756 11282 11288 -1 T - \n", + "86456 812805 11283 11289 -1 C - \n", + "86456 812923 11284 11290 -1 T - \n", + "86456 813004 11285 11291 -1 G - \n", + "86456 813082 11286 11292 -1 G - \n", + "86456 813200 11287 11293 -1 T - \n", + "86456 813299 11288 11294 -1 T - \n", + "86456 813396 11289 11295 -1 T - \n", + "86456 813465 11290 11296 -1 T - \n", + "86456 988872 14670 14676 -1 C T \n", + "86456 1017218 15273 15279 -1 C T \n", + "86456 1058632 16169 16176 -1 T C \n", + "86456 1376533 21756 21765 -1 T - \n", + "86456 1378903 21757 21766 -1 A - \n", + "86456 1381172 21758 21767 -1 C - \n", + "86456 1382119 21759 21768 -1 A - \n", + "86456 1382846 21760 21769 -1 T - \n", + "86456 1383629 21761 21770 -1 G - \n", + "86456 1417048 21982 21991 -1 T - \n", + "86456 1419884 21983 21992 -1 T - \n", + "86456 1422765 21984 21993 -1 A - \n", + "86456 1521333 23054 23063 -1 A T \n", + "86456 1532177 23262 23271 -1 C A \n", + "86456 1554236 23595 23604 -1 C A \n", + "86456 1564585 23700 23709 -1 C T \n", + "86456 1614751 24497 24506 -1 T G \n", + "86456 1634436 24905 24914 -1 G C \n", + "86456 1936829 27962 27972 -1 C T \n", + "86456 1946180 28038 28048 -1 G T \n", + "86456 1960007 28101 28111 -1 A G \n", + "86456 1980201 28261 28271 -1 A - \n", + "86456 2063144 28967 28977 -1 C T \n", + "\n", + " date \n", + "node \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 " + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "alpha_origin_mutations = dfm.loc[alpha_origin[\"node_id\"]]\n", + "alpha_origin_mutations" + ] + }, + { + "cell_type": "markdown", + "id": "74291f64-b6cf-4aee-a494-207251e72feb", + "metadata": {}, + "source": [ + "Here we can see there's quite a lot of mutations (36), but many of them have the derived state of the gap character (\"-\"). These represent the approximation of deletions in sc2ts, in which deletions at each site are modelled indepenently. \n", + "\n", + "We can extract the actual deletion events from this representation by looking at runs of mutations to the gap character and extracting their start and length. We do this using some pandas group-by logic." + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "4796462f-d397-403c-9ca3-749c0a87778f", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "data": { + "text/html": "
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mutation_idsite_idpositionparentinherited_statederived_statedaterun
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\n
", + "text/plain": [ + " mutation_id site_id position parent inherited_state derived_state \\\n", + "node \n", + "86456 812756 11282 11288 -1 T - \n", + "86456 812805 11283 11289 -1 C - \n", + "86456 812923 11284 11290 -1 T - \n", + "86456 813004 11285 11291 -1 G - \n", + "86456 813082 11286 11292 -1 G - \n", + "86456 813200 11287 11293 -1 T - \n", + "86456 813299 11288 11294 -1 T - \n", + "86456 813396 11289 11295 -1 T - \n", + "86456 813465 11290 11296 -1 T - \n", + "86456 1376533 21756 21765 -1 T - \n", + "86456 1378903 21757 21766 -1 A - \n", + "86456 1381172 21758 21767 -1 C - \n", + "86456 1382119 21759 21768 -1 A - \n", + "86456 1382846 21760 21769 -1 T - \n", + "86456 1383629 21761 21770 -1 G - \n", + "86456 1417048 21982 21991 -1 T - \n", + "86456 1419884 21983 21992 -1 T - \n", + "86456 1422765 21984 21993 -1 A - \n", + "86456 1980201 28261 28271 -1 A - \n", + "\n", + " date run \n", + "node \n", + "86456 2020-05-29 1 \n", + "86456 2020-05-29 1 \n", + "86456 2020-05-29 1 \n", + "86456 2020-05-29 1 \n", + "86456 2020-05-29 1 \n", + "86456 2020-05-29 1 \n", + "86456 2020-05-29 1 \n", + "86456 2020-05-29 1 \n", + "86456 2020-05-29 1 \n", + "86456 2020-05-29 2 \n", + "86456 2020-05-29 2 \n", + "86456 2020-05-29 2 \n", + "86456 2020-05-29 2 \n", + "86456 2020-05-29 2 \n", + "86456 2020-05-29 2 \n", + "86456 2020-05-29 3 \n", + "86456 2020-05-29 3 \n", + "86456 2020-05-29 3 \n", + "86456 2020-05-29 4 " + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dels = alpha_origin_mutations[alpha_origin_mutations[\"derived_state\"] == \"-\"].copy()\n", + "dels[\"run\"] = (dels[\"position\"].diff(1) != 1).cumsum()\n", + "dels" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "c1c9bfec-f7b5-45cc-969a-84bbb66a141e", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": "
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
positionlength
run
1112889
2217656
3219913
4282711
\n
", + "text/plain": [ + " position length\n", + "run \n", + "1 11288 9\n", + "2 21765 6\n", + "3 21991 3\n", + "4 28271 1" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dels_grp = dels.groupby(\"run\")\n", + "summary = dels_grp.first() \n", + "summary[\"length\"] = dels_grp.last()[\"position\"] - summary[\"position\"] + 1\n", + "summary[[\"position\", \"length\"]]" + ] + }, + { + "cell_type": "markdown", + "id": "f8ba97a2-bd7e-413f-b7f8-cba70935e8c6", + "metadata": {}, + "source": [ + "So, we have 4 deletions: a 9 bp deletion starting at position 11288, 6bp at 21765, etc.\n", + "\n", + "Non deletions are more straightforward to analyse, but it's important to factor out the deletions first because of their multibase nature. This is easily done:" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "5cdf4a0b-38ac-432c-bafa-6917ff3bf830", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": "
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mutation_idsite_idpositionparentinherited_statederived_statedate
node
86456160960910913-1CT2020-05-29
8645647235353855388-1CA2020-05-29
8645650774759835986-1CT2020-05-29
8645657504569516954-1TC2020-05-29
864569888721467014676-1CT2020-05-29
8645610172181527315279-1CT2020-05-29
8645610586321616916176-1TC2020-05-29
8645615213332305423063-1AT2020-05-29
8645615321772326223271-1CA2020-05-29
8645615542362359523604-1CA2020-05-29
8645615645852370023709-1CT2020-05-29
8645616147512449724506-1TG2020-05-29
8645616344362490524914-1GC2020-05-29
8645619368292796227972-1CT2020-05-29
8645619461802803828048-1GT2020-05-29
8645619600072810128111-1AG2020-05-29
8645620631442896728977-1CT2020-05-29
\n
", + "text/plain": [ + " mutation_id site_id position parent inherited_state derived_state \\\n", + "node \n", + "86456 160960 910 913 -1 C T \n", + "86456 472353 5385 5388 -1 C A \n", + "86456 507747 5983 5986 -1 C T \n", + "86456 575045 6951 6954 -1 T C \n", + "86456 988872 14670 14676 -1 C T \n", + "86456 1017218 15273 15279 -1 C T \n", + "86456 1058632 16169 16176 -1 T C \n", + "86456 1521333 23054 23063 -1 A T \n", + "86456 1532177 23262 23271 -1 C A \n", + "86456 1554236 23595 23604 -1 C A \n", + "86456 1564585 23700 23709 -1 C T \n", + "86456 1614751 24497 24506 -1 T G \n", + "86456 1634436 24905 24914 -1 G C \n", + "86456 1936829 27962 27972 -1 C T \n", + "86456 1946180 28038 28048 -1 G T \n", + "86456 1960007 28101 28111 -1 A G \n", + "86456 2063144 28967 28977 -1 C T \n", + "\n", + " date \n", + "node \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 \n", + "86456 2020-05-29 " + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "non_dels = alpha_origin_mutations[alpha_origin_mutations[\"derived_state\"] != \"-\"]\n", + "non_dels" + ] + }, + { + "cell_type": "markdown", + "id": "a25fef88-9c5e-4ead-aa67-981541a1626e", + "metadata": {}, + "source": [ + "## Recombination nodes and local trees\n", + "\n", + "The ``node_data`` dataframe has a field ``is_recombinant`` which makes finding the recombination nodes in the sc2ts ARG easy" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "9a98fe82-d3e9-48c1-a467-390be51a2012", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": "
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pangosample_idscorpionode_idis_sampleis_recombinantnum_mutationsdatetime
1530B.1.157.1530FalseTrue22020-03-181070.000000
26465B.1.221.26465FalseTrue22020-06-29967.212654
27003B.1.160.27003FalseTrue12020-07-12954.666560
28379B.1.426.28379FalseTrue02020-08-28907.000000
34811B.1.177.34811FalseTrue22020-09-18886.080636
..............................
1430261BA.2Omicron (BA.2-like)1430261FalseTrue112023-01-2131.669198
1430452BA.2Omicron (BA.2-like)1430452FalseTrue22023-01-0349.963285
1431988CH.1.1Omicron (BA.2-like)1431988FalseTrue32023-01-2527.092445
1432902BA.2Omicron (BA.2-like)1432902FalseTrue122023-01-2725.713623
1436032XBB.1.5.4Omicron (XBB.1.5-like)1436032FalseTrue22022-10-09135.913179
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855 rows × 9 columns

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", + "text/plain": [ + " pango sample_id scorpio node_id is_sample \\\n", + "1530 B.1.157 . 1530 False \n", + "26465 B.1.221 . 26465 False \n", + "27003 B.1.160 . 27003 False \n", + "28379 B.1.426 . 28379 False \n", + "34811 B.1.177 . 34811 False \n", + "... ... ... ... ... ... \n", + "1430261 BA.2 Omicron (BA.2-like) 1430261 False \n", + "1430452 BA.2 Omicron (BA.2-like) 1430452 False \n", + "1431988 CH.1.1 Omicron (BA.2-like) 1431988 False \n", + "1432902 BA.2 Omicron (BA.2-like) 1432902 False \n", + "1436032 XBB.1.5.4 Omicron (XBB.1.5-like) 1436032 False \n", + "\n", + " is_recombinant num_mutations date time \n", + "1530 True 2 2020-03-18 1070.000000 \n", + "26465 True 2 2020-06-29 967.212654 \n", + "27003 True 1 2020-07-12 954.666560 \n", + "28379 True 0 2020-08-28 907.000000 \n", + "34811 True 2 2020-09-18 886.080636 \n", + "... ... ... ... ... \n", + "1430261 True 11 2023-01-21 31.669198 \n", + "1430452 True 2 2023-01-03 49.963285 \n", + "1431988 True 3 2023-01-25 27.092445 \n", + "1432902 True 12 2023-01-27 25.713623 \n", + "1436032 True 2 2022-10-09 135.913179 \n", + "\n", + "[855 rows x 9 columns]" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df_recomb = dfn[dfn.is_recombinant]\n", + "df_recomb" + ] + }, + { + "cell_type": "markdown", + "id": "6a5af3d4-3119-45a3-8a9e-773be9b76d2c", + "metadata": {}, + "source": [ + "XBB is an important recombinant and is well captured by the sc2ts ARG. Its \"origin node\" is a recombination node, meaning that it has more than one parent in the ARG. We can see that the ``is_recombinant`` flag is True:" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "0769825e-91c3-4519-8481-aca210914ca2", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "sample_id \n", + "scorpio Omicron (XBB-like)\n", + "node_id 1396207\n", + "is_sample False\n", + "is_recombinant True\n", + "num_mutations 14\n", + "date 2022-05-30 00:00:00\n", + "time 267.175348\n", + "Name: XBB, dtype: object" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "xbb_origin = dfn_pango.loc[\"XBB\"]\n", + "xbb_origin" + ] + }, + { + "cell_type": "markdown", + "id": "215bfb5b-c70d-4b87-bca4-edfd5c51e815", + "metadata": {}, + "source": [ + "To find where the breakpoint is (all recombinants in the current sc2ts ARG have only 2 parents and consequently one breakpoint; this is not a limitation of tskit, which allows arbitrarily complex inheritance), we must inspect the tskit [edge table](https://tskit.dev/tskit/docs/stable/data-model.html#edge-table). This simply records the IDs of the parent and child nodes and the interval over which this relationship applies. We then find the edges which record the parents of the XBB origin by looking for those edges in which it is a child:" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "c15e4fcc-1243-470d-900c-b9828d271bd7", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([235736, 400939])" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "xbb_edges = np.where(ts.edges_child == xbb_origin[\"node_id\"])[0]\n", + "xbb_edges" + ] + }, + { + "cell_type": "markdown", + "id": "055ade7e-43c9-43bc-bc3a-34c26c239508", + "metadata": {}, + "source": [ + "We get two edge IDs, which we can then use to get the properties of the edges themselves. One quick way to visualise the information is to access the edge table directly:" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "c4b3f384-5772-4200-ba6a-5c8ad7e8dbf0", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": "\n
\n \n \n \n \n \n \n \n \n \n\n\n \n
idleftrightparentchildmetadata
022,57729,9041,363,9391,396,207
1022,5771,101,9421,396,207
\n
\n ", + "text/plain": [ + "" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ts.tables.edges[xbb_edges]" + ] + }, + { + "cell_type": "markdown", + "id": "6546cb1d-7401-4305-94bf-34a77c219802", + "metadata": {}, + "source": [ + "We can also look at the parents of the event directly:" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "id": "e24c19c4-70b8-4ca5-b705-ea6548a2e7f6", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": "
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
pangosample_idscorpionode_idis_sampleis_recombinantnum_mutationsdatetime
1363939BM.1.1.1Omicron (BA.2-like)1363939FalseFalse12022-04-26301.500484
1101942BA.2.10ERR9201084Omicron (BA.2-like)1101942TrueFalse12022-02-26360.000000
\n
", + "text/plain": [ + " pango sample_id scorpio node_id is_sample \\\n", + "1363939 BM.1.1.1 Omicron (BA.2-like) 1363939 False \n", + "1101942 BA.2.10 ERR9201084 Omicron (BA.2-like) 1101942 True \n", + "\n", + " is_recombinant num_mutations date time \n", + "1363939 False 1 2022-04-26 301.500484 \n", + "1101942 False 1 2022-02-26 360.000000 " + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dfn.loc[ts.edges_parent[xbb_edges]]" + ] + }, + { + "cell_type": "markdown", + "id": "6b37bfe1-806f-41b0-ba81-b7c38d048d52", + "metadata": {}, + "source": [ + "To get the breakpoint, we can then take the maximum of the left coordinate:\n", + "\n", + "(Note, we're using two different conventions for accessing the underlying table data here --- they are essentially equivalent and can be mixed and matched as is most convenient.)" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "93f84fb1-1c2d-48c6-80b9-bae9ee75f8e2", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "np.float64(22577.0)" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "bp = np.max(ts.edges_left[xbb_edges])\n", + "bp" + ] + }, + { + "cell_type": "markdown", + "id": "7b24be24-6d34-40fa-99c4-50066d6f9204", + "metadata": {}, + "source": [ + "The *effect* of this recombination event is to change the tree to the left and right of the breakpoint. Tskit provides an efficient view over the \"local trees\" along the genome that result from recombination events. In this case, we would like to examine the trees to the right and left of the breakpoint for XBB. The simplest (and most efficient) way to do this is to first look at the right-hand tree using the ``ts.at`` method. " + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "id": "885752df-91d5-4f48-b0e9-630524e0ba5f", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": "\n
\n \n
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\n \n Tree \n
Index193
Interval22 577-22 578 (1)
Roots1
Nodes2 747 984
Sites1
Mutations87
Total Branch Length99 256 253
\n
\n
\n
\n ", + "text/plain": [ + "" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tree = ts.at(bp)\n", + "tree" + ] + }, + { + "cell_type": "markdown", + "id": "ed928d34-e748-4978-b451-02497a3e88a0", + "metadata": {}, + "source": [ + "The tree returned here is an instance of the tskit [Tree](https://tskit.dev/tskit/docs/stable/python-api.html#tskit.Tree) class which provides many operations. This is built around the efficient numerical representation of trees, and specifically, the \n", + "[quintuply linked tree](https://tskit.dev/tskit/docs/stable/data-model.html#quintuply-linked-trees) data structure, in which the tree topology is encoded using a set of numpy arrays. For example, the parent of each node in the tree is represented using the ``parent_array``:" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "id": "7c4ea418-38fb-4bf4-8f12-3ef952a3174f", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([ -1, -1, 9, ..., 2740283, 2736794, -1],\n", + " shape=(2747986,), dtype=int32)" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tree.parent_array" + ] + }, + { + "cell_type": "markdown", + "id": "002a96e1-7626-42ef-8e45-30c54af1df90", + "metadata": {}, + "source": [ + "So, ``tree.parent_array[u]`` means \"what is the node ID of the parent of node ``u`` in this tree\". The ``-1`` values here indicate that a particular node has no parent, and so is either a root or is not \"present\" in the current tree. We can then verify that the local tree has the correct parent for the right-hand side of the XBB recombination event:" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "id": "16d868b9-016c-4bfe-aa03-99f4c34fb4f5", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "np.int32(1363939)" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tree.parent_array[xbb_origin[\"node_id\"]]" + ] + }, + { + "cell_type": "markdown", + "id": "75585ae4-c597-451c-a60b-d9dc940cc949", + "metadata": {}, + "source": [ + "We can use the same approach to access the tree on the left hand side of the breakpoint, but it is more efficient to \"mutate\" the current tree instance using the ``prev()`` method. This is because ``ts.at()`` requires us to create a new tree instance and to apply all the edges that intersect with the given point. Using the ``prev`` method, on the other hand, takes advantage of the fact that there's very little difference between the trees at either side of the breakpoint and makes those minimal changes." + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "id": "414c9f6b-55c2-4e04-86e2-3ad0f47fb398", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": "\n
\n \n
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\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
\n \n Tree \n
Index192
Interval22 502-22 577 (75)
Roots1
Nodes2 747 984
Sites75
Mutations3 043
Total Branch Length99 256 311
\n
\n
\n
\n ", + "text/plain": [ + "" + ] + }, + "execution_count": 22, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tree.prev()\n", + "tree" + ] + }, + { + "cell_type": "markdown", + "id": "28d0dccd-dd49-4555-a193-768a6ab69381", + "metadata": {}, + "source": [ + "Now we can also verify that the left-hand parent of the XBB recombination node is what we extracted from the node table above." + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "id": "14412fce-b232-4fef-8c13-7d4a23fe7db7", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "np.int32(1101942)" + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tree.parent_array[xbb_origin[\"node_id\"]]" + ] + }, + { + "cell_type": "markdown", + "id": "d4bb9e82-7305-4902-a3af-42c93e4eca87", + "metadata": {}, + "source": [ + "## Getting the ancestors of a node in a tree\n", + "\n", + "An operation that we're often interested in is to get the ancestors of a node in a particular tree. Using the ``ancestors`` methods along with Pandas selection provides an easy way to access data on the ancestors of the Alpha origin node." + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "id": "afdc9ad6-5fcd-4c72-b37e-502950e0564c", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "data": { + "text/html": "
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
pangosample_idscorpionode_idis_sampleis_recombinantnum_mutationsdatetime
86456B.1.1.7Alpha (B.1.1.7-like)86456FalseFalse362020-09-23881.613313
4552B.1.1.4552FalseFalse32020-02-031114.859379
98B.1.1.98FalseFalse32020-01-281120.000555
59B.1.59FalseFalse12020-01-281120.059657
12B.1SRR11597205.12TrueFalse22020-01-281120.059657
27B.27FalseFalse12019-12-261153.000000
1BWuhan/Hu-1/2019.1FalseFalse02019-12-261153.000000
\n
", + "text/plain": [ + " pango sample_id scorpio node_id is_sample \\\n", + "86456 B.1.1.7 Alpha (B.1.1.7-like) 86456 False \n", + "4552 B.1.1 . 4552 False \n", + "98 B.1.1 . 98 False \n", + "59 B.1 . 59 False \n", + "12 B.1 SRR11597205 . 12 True \n", + "27 B . 27 False \n", + "1 B Wuhan/Hu-1/2019 . 1 False \n", + "\n", + " is_recombinant num_mutations date time \n", + "86456 False 36 2020-09-23 881.613313 \n", + "4552 False 3 2020-02-03 1114.859379 \n", + "98 False 3 2020-01-28 1120.000555 \n", + "59 False 1 2020-01-28 1120.059657 \n", + "12 False 2 2020-01-28 1120.059657 \n", + "27 False 1 2019-12-26 1153.000000 \n", + "1 False 0 2019-12-26 1153.000000 " + ] + }, + "execution_count": 24, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tree = ts.first() \n", + "u = alpha_origin[\"node_id\"]\n", + "dfn.iloc[[u] + list(tree.ancestors(u))] " + ] + }, + { + "cell_type": "markdown", + "id": "743c6e7e-b05b-4ca2-b3c9-37ef4bbb2f8e", + "metadata": {}, + "source": [ + "**Note:** In this example we use the first tree in the sequence to access the ancestors of the Alpha origin node. This is valid here because there is no recombinant among those ancestors. When recombination is present among the ancestors, more care is required." + ] + }, + { + "cell_type": "markdown", + "id": "a554af7a-ff2d-420f-9128-7398cda148f9", + "metadata": {}, + "source": [ + "## Iterating over all trees\n", + "\n", + "A common pattern in analysing ARGs with tskit is to iterate sequentially over all local trees along the genome. This is done using the ``.trees()`` iterator, which again takes advantage of the fact that adjacent trees are very similar for efficiency. Here we use this to count the number of polytomies (nodes with > 2 children) in each local tree. This is done using Numpy functions on the ``num_children_array``, which is a zero-copy view on a per-node count maintained by the underlying C library." + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "id": "0b964893-7eae-442c-9d15-a1ebb62a0743", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "CPU times: user 915 ms, sys: 32 ms, total: 947 ms\n", + "Wall time: 946 ms\n" + ] + }, + { + "data": { + "text/plain": [ + "(np.int64(222242), np.int64(222257))" + ] + }, + "execution_count": 25, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "%%time\n", + "num_polytomies = np.zeros(ts.num_trees, dtype=int)\n", + "for tree in ts.trees():\n", + " num_polytomies[tree.index] = np.sum(tree.num_children_array > 2)\n", + "np.min(num_polytomies), np.max(num_polytomies)" + ] + }, + { + "cell_type": "markdown", + "id": "69fadfc9-5751-4f30-bba7-62db18ae6bf6", + "metadata": {}, + "source": [ + "## Examining children\n", + "\n", + "The numpy ``argmax`` function gives us a conveient way to find the ID of the node which has the largest number of children:" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "id": "4f335212-f257-4448-9bc1-997fc7a8191b", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "data": { + "text/plain": [ + "np.int32(12682)" + ] + }, + "execution_count": 26, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tree = ts.first()\n", + "u = np.argmax(tree.num_children_array)\n", + "tree.num_children_array[u]" + ] + }, + { + "cell_type": "markdown", + "id": "b5c96340-983c-40a0-8d30-e7d1f36695ab", + "metadata": {}, + "source": [ + "This has an impressive 12,682 children! We can first look at its path back to root, and verify that it is valid across all trees by checking that there are no recombinants in its ancestry:" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "id": "6d57ceab-1470-4d1d-9130-5c9bfe252f05", + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "data": { + "text/html": "
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pangosample_idscorpionode_idis_sampleis_recombinantnum_mutationsdatetime
887654BA.2.5Omicron (BA.2-like)887654FalseFalse12021-11-11467.306208
863361BA.2Omicron (BA.2-like)863361FalseFalse22021-11-05473.128012
843826BA.2Omicron (BA.2-like)843826FalseFalse02021-11-05473.128012
822854BA.2Omicron (BA.2-like)822854FalseFalse422021-11-05473.128012
1436802B.1.1.529Probable Omicron (Unassigned)1436802FalseFalse392020-06-26970.041636
759815B.1.1.759815FalseFalse12020-01-281120.000353
5001B.1.1.5001FalseFalse12020-01-281120.000353
98B.1.1.98FalseFalse32020-01-281120.000555
59B.1.59FalseFalse12020-01-281120.059657
12B.1SRR11597205.12TrueFalse22020-01-281120.059657
27B.27FalseFalse12019-12-261153.000000
1BWuhan/Hu-1/2019.1FalseFalse02019-12-261153.000000
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", + "text/plain": [ + " pango sample_id scorpio node_id \\\n", + "887654 BA.2.5 Omicron (BA.2-like) 887654 \n", + "863361 BA.2 Omicron (BA.2-like) 863361 \n", + "843826 BA.2 Omicron (BA.2-like) 843826 \n", + "822854 BA.2 Omicron (BA.2-like) 822854 \n", + "1436802 B.1.1.529 Probable Omicron (Unassigned) 1436802 \n", + "759815 B.1.1 . 759815 \n", + "5001 B.1.1 . 5001 \n", + "98 B.1.1 . 98 \n", + "59 B.1 . 59 \n", + "12 B.1 SRR11597205 . 12 \n", + "27 B . 27 \n", + "1 B Wuhan/Hu-1/2019 . 1 \n", + "\n", + " is_sample is_recombinant num_mutations date time \n", + "887654 False False 1 2021-11-11 467.306208 \n", + "863361 False False 2 2021-11-05 473.128012 \n", + "843826 False False 0 2021-11-05 473.128012 \n", + "822854 False False 42 2021-11-05 473.128012 \n", + "1436802 False False 39 2020-06-26 970.041636 \n", + "759815 False False 1 2020-01-28 1120.000353 \n", + "5001 False False 1 2020-01-28 1120.000353 \n", + "98 False False 3 2020-01-28 1120.000555 \n", + "59 False False 1 2020-01-28 1120.059657 \n", + "12 True False 2 2020-01-28 1120.059657 \n", + "27 False False 1 2019-12-26 1153.000000 \n", + "1 False False 0 2019-12-26 1153.000000 " + ] + }, + "execution_count": 27, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dfn.loc[[u] + list(tree.ancestors(u))]" + ] + }, + { + "cell_type": "markdown", + "id": "296288b0-5a55-46d8-92e4-a834bb7ba17d", + "metadata": {}, + "source": [ + "We can then get the list of children for that node using the ``tree.children()`` method, and extract the relevant rows from the node data table:" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "id": "6ebe4cc4-a419-443f-9d23-4253daf369c1", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": "
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pangosample_idscorpionode_idis_sampleis_recombinantnum_mutationsdatetime
886829BA.2.5SRR17712991Omicron (BA.2-like)886829TrueFalse02021-12-13435.000000
903506BA.2.5Omicron (BA.2-like)903506FalseFalse12021-11-11467.306208
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", + "text/plain": [ + " pango sample_id scorpio node_id is_sample \\\n", + "886829 BA.2.5 SRR17712991 Omicron (BA.2-like) 886829 True \n", + "903506 BA.2.5 Omicron (BA.2-like) 903506 False \n", + "924867 BA.2 SRR17712363 Omicron (BA.2-like) 924867 True \n", + "927976 BA.2 ERR9234047 Omicron (BA.2-like) 927976 True \n", + "927977 BA.2 ERR9234055 Omicron (BA.2-like) 927977 True \n", + "... ... ... ... ... ... \n", + "2735525 BA.2 Omicron (BA.2-like) 2735525 False \n", + "2739602 BA.2 Omicron (BA.2-like) 2739602 False \n", + "2742229 BA.2 Omicron (BA.2-like) 2742229 False \n", + "2742596 BA.2 Omicron (BA.2-like) 2742596 False \n", + "2744062 BA.2 Omicron (BA.2-like) 2744062 False \n", + "\n", + " is_recombinant num_mutations date time \n", + "886829 False 0 2021-12-13 435.000000 \n", + "903506 False 1 2021-11-11 467.306208 \n", + "924867 False 2 2021-12-30 418.000000 \n", + "927976 False 1 2022-01-02 415.000000 \n", + "927977 False 1 2022-01-02 415.000000 \n", + "... ... ... ... ... \n", + "2735525 False 1 2021-12-21 427.140858 \n", + "2739602 False 1 2021-12-16 432.996202 \n", + "2742229 False 1 2022-02-25 361.765177 \n", + "2742596 False 1 2022-01-04 413.235262 \n", + "2744062 False 1 2021-12-26 422.631339 \n", + "\n", + "[12682 rows x 9 columns]" + ] + }, + "execution_count": 28, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df_children = dfn.loc[list(tree.children(u))]\n", + "df_children" + ] + }, + { + "cell_type": "markdown", + "id": "83074085-d954-4036-977f-c3127e483286", + "metadata": {}, + "source": [ + "When we break down the counts of those nodes by their sample status and number of mutations, we see that we have over 9,500 samples which are identical to the focal node. Thus, this seems like a well-inferred node capturing a very deeply sampled phase of the BA.2 outbreak." + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "id": "edd47997-53a5-4970-85f7-792b169513e9", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "num_mutations is_sample\n", + "0 True 9552\n", + "1 True 2038\n", + " False 816\n", + "2 True 198\n", + " False 36\n", + "3 True 28\n", + "4 True 7\n", + "3 False 4\n", + "5 True 2\n", + "6 False 1\n", + "Name: count, dtype: int64" + ] + }, + "execution_count": 29, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df_children[[\"num_mutations\", \"is_sample\"]].value_counts()" + ] + }, + { + "cell_type": "markdown", + "id": "f41c520a-b5d2-40b6-82e4-5690654bb088", + "metadata": {}, + "source": [ + "## All descendants\n", + "\n", + "Getting the descendants of a node in a particular tree is straightforward, and can be done efficiently in the standard traversal orders. For example, here we get all the nodes descending from the Alpha origin in the first tree in preorder, and extract the corresponding dataframe:\n" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "id": "210941b9-045c-4335-9e09-5833e5e0f525", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([ 86456, 45989, 45958, ..., 1551400, 1551420, 86035],\n", + " shape=(317368,), dtype=int32)" + ] + }, + "execution_count": 30, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tree = ts.first()\n", + "descendants = tree.preorder(alpha_origin[\"node_id\"])\n", + "descendants" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "id": "8afeb231-a627-43ff-b39c-576c14ee3236", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": "
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", + "text/plain": [ + " pango sample_id scorpio node_id is_sample \\\n", + "86456 B.1.1.7 Alpha (B.1.1.7-like) 86456 False \n", + "45989 B.1.1.7 Alpha (B.1.1.7-like) 45989 False \n", + "45958 B.1.1.7 ERR4827009 Alpha (B.1.1.7-like) 45958 True \n", + "51925 B.1.1.7 ERR4862251 Alpha (B.1.1.7-like) 51925 True \n", + "56457 B.1.1.7 ERR4905821 Alpha (B.1.1.7-like) 56457 True \n", + "... ... ... ... ... ... \n", + "1543606 B.1.1.7 ERR5316249 Alpha (B.1.1.7-like) 1543606 True \n", + "1544098 B.1.1.7 ERR5314092 Alpha (B.1.1.7-like) 1544098 True \n", + "1551400 B.1.1.7 ERR5338932 Alpha (B.1.1.7-like) 1551400 True \n", + "1551420 B.1.1.7 ERR5338978 Alpha (B.1.1.7-like) 1551420 True \n", + "86035 B.1.1.7 ERR5178290 Alpha (B.1.1.7-like) 86035 True \n", + "\n", + " is_recombinant num_mutations date time \n", + "86456 False 36 2020-09-23 881.613313 \n", + "45989 False 1 2020-09-23 881.613313 \n", + "45958 False 1 2020-10-21 853.000000 \n", + "51925 False 1 2020-11-05 838.000000 \n", + "56457 False 1 2020-11-11 832.000000 \n", + "... ... ... ... ... \n", + "1543606 False 0 2021-02-05 746.000000 \n", + "1544098 False 0 2021-02-06 745.000000 \n", + "1551400 False 0 2021-02-13 738.000000 \n", + "1551420 False 0 2021-02-13 738.000000 \n", + "86035 False 0 2020-12-29 784.000000 \n", + "\n", + "[317368 rows x 9 columns]" + ] + }, + "execution_count": 31, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "alpha_descendants = dfn.loc[descendants]\n", + "alpha_descendants" + ] + }, + { + "cell_type": "markdown", + "id": "218f3e48-b9a2-48a4-97ac-50ac835fc53e", + "metadata": {}, + "source": [ + "However, this is an approximation to the true descendants of the node, because there are some recombinants descending from it. " + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "id": "c503ac3a-625f-4694-b0c8-ca271027b483", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": "
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", + "text/plain": [ + " pango sample_id scorpio node_id is_sample \\\n", + "263782 B.1.526 Iota (B.1.526-like) 263782 False \n", + "277217 B.1.1.7 Alpha (B.1.1.7-like) 277217 False \n", + "251428 B.1.1.7 Alpha (B.1.1.7-like) 251428 False \n", + "330618 Q.3 Alpha (B.1.1.7-like) 330618 False \n", + "229637 B.1.1.7 Alpha (B.1.1.7-like) 229637 False \n", + "191383 B.1.1.7 Alpha (B.1.1.7-like) 191383 False \n", + "214402 B.1.1.7 Alpha (B.1.1.7-like) 214402 False \n", + "104754 B.1.177.9 . 104754 False \n", + "143250 B.1.1.7 Alpha (B.1.1.7-like) 143250 False \n", + "286975 B.1.1.7 Alpha (B.1.1.7-like) 286975 False \n", + "179752 B.1.1.7 Alpha (B.1.1.7-like) 179752 False \n", + "254203 B.1.526 Iota (B.1.526-like) 254203 False \n", + "238621 B.1.1.7 Alpha (B.1.1.7-like) 238621 False \n", + "213224 B.1.1.7 Alpha (B.1.1.7-like) 213224 False \n", + "237642 B.1.1.7 Alpha (B.1.1.7-like) 237642 False \n", + "105931 B.1.1.7 . 105931 False \n", + "153040 B.1.1.7 Alpha (B.1.1.7-like) 153040 False \n", + "\n", + " is_recombinant num_mutations date time \n", + "263782 True 2 2021-04-05 687.738310 \n", + "277217 True 0 2021-05-12 650.000000 \n", + "251428 True 3 2021-04-14 678.320265 \n", + "330618 True 1 2021-07-01 600.596459 \n", + "229637 True 1 2021-03-28 695.635514 \n", + "191383 True 0 2021-02-28 723.309391 \n", + "214402 True 2 2021-03-27 696.000000 \n", + "104754 True 3 2021-01-07 775.258650 \n", + "143250 True 2 2021-02-04 747.485300 \n", + "286975 True 1 2021-05-19 643.294881 \n", + "179752 True 2 2021-02-16 735.853266 \n", + "254203 True 1 2021-04-16 676.041004 \n", + "238621 True 0 2021-03-01 722.000000 \n", + "213224 True 2 2021-03-21 702.000000 \n", + "237642 True 2 2021-03-20 703.287879 \n", + "105931 True 0 2020-12-10 803.000000 \n", + "153040 True 2 2021-02-16 735.000000 " + ] + }, + "execution_count": 32, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "alpha_descendants[alpha_descendants[\"is_recombinant\"]]" + ] + }, + { + "cell_type": "markdown", + "id": "20150dd8-a1b4-4380-91a4-0bb05e6bd760", + "metadata": {}, + "source": [ + "To get the true set of descendants of this node we must currently take the union of the descendants across all trees as follows.\n", + "\n", + "**NOTE:** efficient support for this operation is planned in tskit" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "id": "c704ac47-409e-4c26-bea6-47f558617f5d", + "metadata": {}, + "outputs": [], + "source": [ + "all_descendants = []\n", + "for tree in ts.trees():\n", + " all_descendants = np.union1d(\n", + " all_descendants, np.sort(tree.preorder(alpha_origin[\"node_id\"])))" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "id": "c874a4ea-2c49-4f01-9770-e3b4e5cfb343", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": "
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0000000..3316b88 --- /dev/null +++ b/pyodide-custom-recipes/humanize/meta.yaml @@ -0,0 +1,16 @@ +package: + name: humanize + version: 4.14.0 + top-level: + - humanize + +source: + url: https://files.pythonhosted.org/packages/c3/5b/9512c5fb6c8218332b530f13500c6ff5f3ce3342f35e0dd7be9ac3856fd3/humanize-4.14.0-py3-none-any.whl + sha256: d57701248d040ad456092820e6fde56c930f17749956ac47f4f655c0c547bfff + +about: + home: https://github.com/python-humanize/humanize + PyPI: https://pypi.org/project/humanize + summary: Python humanize utilities + license: MIT + diff --git a/pyodide-custom-recipes/sc2ts/meta.yaml b/pyodide-custom-recipes/sc2ts/meta.yaml new file mode 100644 index 0000000..89bb2bf --- /dev/null +++ b/pyodide-custom-recipes/sc2ts/meta.yaml @@ -0,0 +1,27 @@ +package: + name: sc2ts + version: 1.0.1 + top-level: + - sc2ts + +source: + url: https://files.pythonhosted.org/packages/7d/b7/763bfbd2a4bbaa810acdbffdb24acd4bcecacc2de0786f5f011a058b1005/sc2ts-1.0.1-py3-none-any.whl + sha256: 639ea91a515e7fd19914ecad3d2c6e36694b62f14e70fad45f24a832f409600b + +requirements: + run: + - tskit + - tszip + - pandas + - tqdm + - zarr + - click + - tomli + - humanize + +about: + home: https://tskit.dev/sc2ts + PyPI: https://pypi.org/project/sc2ts + summary: Infer ARGs for SARS-CoV-2 in tskit format + license: GPL-3.0-or-later + diff --git a/pyodide-custom-recipes/tszip/meta.yaml b/pyodide-custom-recipes/tszip/meta.yaml new file mode 100644 index 0000000..c5105e6 --- /dev/null +++ b/pyodide-custom-recipes/tszip/meta.yaml @@ -0,0 +1,26 @@ +package: + name: tszip + version: 0.2.6 + tag: + - always + top-level: + - tszip + +source: + url: https://files.pythonhosted.org/packages/70/53/200fba914ebb68ac1f11897fafdb9523238eb0b0f1852529f4a59edcc2d2/tszip-0.2.6-py3-none-any.whl + sha256: 1f2a3568f87b28e7435ec881c49e7e3b9d98d1283b8cec9ca38537ab27ed70bb + +requirements: + run: + - numpy + - humanize + - tskit + - numcodecs + - zarr + +about: + home: https://tskit.dev/tszip + PyPI: https://pypi.org/project/tszip + summary: Compression utilities for tree sequences + license: MIT + diff --git a/pyodide-custom-recipes/zarr/meta.yaml b/pyodide-custom-recipes/zarr/meta.yaml new file mode 100644 index 0000000..1548cb8 --- /dev/null +++ b/pyodide-custom-recipes/zarr/meta.yaml @@ -0,0 +1,21 @@ +package: + name: zarr + version: 2.18.7 + # Keep zarr on a 2.x release; zarr 3.x uses threading, which is not suitable for the Pyodide runtime. + pinned: true + top-level: + - zarr +source: + sha256: ac3dc4033e9ae4e9d7b5e27c97ea3eaf1003cc0a07f010bd83d5134bf8c4b223 + url: https://files.pythonhosted.org/packages/py3/z/zarr/zarr-2.18.7-py3-none-any.whl +requirements: + run: + - numpy + - asciitree + - numcodecs +about: + home: https://github.com/zarr-developers/zarr-python + PyPI: https://pypi.org/project/zarr + summary: An implementation of chunked, compressed, N-dimensional arrays for Python. + license: MIT + diff --git a/tests/test_notebooks_pyodide.py b/tests/test_notebooks_pyodide.py new file mode 100644 index 0000000..1904c0e --- /dev/null +++ b/tests/test_notebooks_pyodide.py @@ -0,0 +1,49 @@ +import json +import os +from pathlib import Path + +import nbformat +from nbclient import NotebookClient + + +ROOT = Path(__file__).resolve().parents[1] +DIST = ROOT / "dist" +PYODIDE_LOCK = DIST / "static" / "pyodide" / "pyodide-lock.json" + + +def test_pyodide_world_contains_expected_packages(): + """Sanity-check that the custom Pyodide world includes key packages.""" + data = json.loads(PYODIDE_LOCK.read_text(encoding="utf8")) + packages = data["packages"] + for name in ["tskit", "numpy", "scipy", "pandas", "msprime", "pysam", "zarr", "humanize", "tszip", "sc2ts"]: + assert name in packages, f"{name} missing from pyodide-lock.json" + + +def _execute_notebook(notebook_path: Path, *, cells: int | None = None, timeout: int = 600) -> None: + """Execute a notebook using the local CPython kernel. + + If `cells` is provided, only the first `cells` code cells are executed. + """ + nb = nbformat.read(notebook_path, as_version=4) + + if cells is not None: + code_cells = [c for c in nb.cells if c.cell_type == "code"] + if code_cells: + nb.cells = code_cells[:cells] + + cwd = os.getcwd() + try: + os.chdir(notebook_path.parent) + client = NotebookClient(nb, timeout=timeout, kernel_name="python3") + client.execute() + finally: + os.chdir(cwd) + + +def test_tskit_notebook_executes(): + _execute_notebook(ROOT / "content" / "tskit.ipynb") + + +def test_sc2ts_notebook_imports_and_loads(): + # Run just the first code cell, which imports tszip/sc2ts and loads the ARG. + _execute_notebook(ROOT / "content" / "sc2ts.ipynb", cells=1, timeout=900) diff --git a/tskit-launcher/package-lock.json b/tskit-launcher/package-lock.json new file mode 100644 index 0000000..a5b16e3 --- /dev/null +++ b/tskit-launcher/package-lock.json @@ -0,0 +1,5776 @@ +{ + "name": "tskit_launcher", + "version": "0.1.0", + "lockfileVersion": 3, + "requires": true, + 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