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Merge pull request #569 from benjeffery/docs
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‎README.md‎

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Resources:
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- See this [notebook](https://github.com/jeromekelleher/sc2ts-paper/blob/main/notebooks/example_data_processing.ipynb)
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- See this [notebook](https://github.com/tskit-dev/sc2ts-paper/blob/main/notebooks/example_data_processing.ipynb)
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for an example in which we access the data variant-by-variant and
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which explains the low-level data encoding
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- See the [VCF Zarr publication](https://doi.org/10.1093/gigascience/giaf049)

‎docs/Makefile‎

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# Need to set PYTHONPATH so that we pick up the local sc2ts
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PYPATH=${PWD}/..
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SC2TS_VERSION:=$(shell PYTHONPATH=${PYPATH} \
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python3 -c 'import sc2ts; print(sc2ts.__version__.split("+")[0])')
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dev:
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PYTHONPATH=${PYPATH} ./build.sh
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dist:
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@echo Building distribution for sc2ts version ${SC2TS_VERSION}
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sed -i s/__SC2TS_VERSION__/${SC2TS_VERSION}/g _config.yml
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PYTHONPATH=${PYPATH} ./build.sh
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clean:
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rm -fR _build
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‎docs/_config.yml‎

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# Book settings
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# Learn more at https://jupyterbook.org/customize/config.html
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title: sc2ts manual
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author: sc2ts developers
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logo: sc2ts.png
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copyright: "2024"
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only_build_toc_files: true
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execute:
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execute_notebooks: cache
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launch_buttons:
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binderhub_url: ""
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repository:
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url: https://github.com/tskit-dev/sc2ts
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branch: main
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path_to_book: docs
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html:
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favicon: sc2ts.png
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use_issues_button: true
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use_repository_button: true
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use_edit_page_button: true
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sphinx:
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extra_extensions:
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- sphinx_copybutton
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- sphinx.ext.autodoc
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- sphinx.ext.autosummary
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- sphinx.ext.todo
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- sphinx.ext.viewcode
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- sphinx.ext.intersphinx
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- sphinx_issues
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- sphinxarg.ext
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- IPython.sphinxext.ipython_console_highlighting
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- sphinx_click.ext
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config:
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html_theme: sphinx_book_theme
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html_theme_options:
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navigation_with_keys: false
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pygments_dark_style: monokai
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logo:
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text: "Version __SC2TS_VERSION__"
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myst_enable_extensions:
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- colon_fence
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- deflist
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- substitution
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issues_github_path: tskit-dev/sc2ts
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todo_include_todos: true
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intersphinx_mapping:
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python: ["https://docs.python.org/3/", null]
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tskit: ["https://tskit.dev/tskit/docs/stable", null]
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tutorials: ["https://tskit.dev/tutorials/", null]
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numpy: ["https://numpy.org/doc/stable/", null]
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pandas: ["https://pandas.pydata.org/docs/", null]
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nitpicky: true
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autodoc_member_order: bysource
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autodoc_typehints: none
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myst_substitutions:
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min_python_version: "3.10"

‎docs/_toc.yml‎

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format: jb-book
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root: intro
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parts:
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- caption: Interfaces
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chapters:
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- file: cli
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- file: api

‎docs/api.md‎

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# Python API
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This page documents the public Python API exposed by ``sc2ts``.
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Inference is driven via the command line interface (see the
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{ref}`CLI documentation <sc2ts_sec_cli>`); the functions and classes
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listed here are intended for working with tree sequences and datasets
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that have already been generated.
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The reference documentation is concise and exhaustive; for higher level
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discussion and worked examples, see the project README and example
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notebooks.
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```{eval-rst}
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.. currentmodule:: sc2ts
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```
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## ARG analysis
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```{eval-rst}
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.. autosummary::
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node_data
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mutation_data
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```
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```{eval-rst}
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.. autofunction:: node_data
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.. autofunction:: mutation_data
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```
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## Dataset access
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```{eval-rst}
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.. autosummary::
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Dataset
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decode_alignment
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mask_ambiguous
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mask_flanking_deletions
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```
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```{eval-rst}
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.. autoclass:: Dataset
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:members:
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.. autofunction:: decode_alignment
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.. autofunction:: mask_ambiguous
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.. autofunction:: mask_flanking_deletions
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```
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## Core constants and helpers
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```{eval-rst}
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.. autosummary::
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REFERENCE_STRAIN
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REFERENCE_DATE
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REFERENCE_GENBANK
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REFERENCE_SEQUENCE_LENGTH
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IUPAC_ALLELES
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decode_flags
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flags_summary
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```
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```{eval-rst}
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.. autodata:: REFERENCE_STRAIN
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.. autodata:: REFERENCE_DATE
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.. autodata:: REFERENCE_GENBANK
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.. autodata:: REFERENCE_SEQUENCE_LENGTH
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.. autodata:: IUPAC_ALLELES
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.. autofunction:: decode_flags
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.. autofunction:: flags_summary
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```

‎docs/build.sh‎

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#/bin/bash
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# Jupyter-build doesn't have an option to automatically show the
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# saved reports, which makes it difficult to debug the reasons for
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# build failures in CI. This is a simple wrapper to handle that.
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REPORTDIR=_build/html/reports
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jupyter-book build .
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RETVAL=$?
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if [ $RETVAL -ne 0 ]; then
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if [ -e $REPORTDIR ]; then
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echo "Error occured; showing saved reports"
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cat $REPORTDIR/*
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fi
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else
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# Clear out any old reports
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rm -f $REPORTDIR/*
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fi
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exit $RETVAL
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‎docs/cli.rst‎

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.. _sc2ts_sec_cli:
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Command line interface
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======================
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The ``sc2ts`` package provides a command line interface for running
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inference and working with sc2ts datasets. After installation, the
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``sc2ts`` entry point should be available::
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$ sc2ts --help
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You can also invoke the CLI via the module::
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$ python -m sc2ts --help
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Order of high-level commands
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----------------------------
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In a typical end-to-end workflow, the main subcommands are used in the
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following order:
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1. ``import-alignments`` and ``import-metadata`` to build a VCF Zarr
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dataset from raw alignments and metadata.
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2. ``infer`` to run primary inference over the dataset and produce a
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series of tree sequence files and a match database.
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3. ``postprocess`` to apply housekeeping steps and incorporate exact
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matches, outputting a cleaned ARG.
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4. ``minimise-metadata`` to generate an analysis-ready ARG with compact
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metadata suitable for use with the Python analysis APIs.
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Below we list all subcommands and options provided by the CLI. This
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output is generated directly from the Click definitions in
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``sc2ts.cli`` using the ``sphinx-click`` extension, and so stays in
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sync with the implementation.
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.. click:: sc2ts.cli:cli
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:prog: sc2ts
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:nested: full

‎docs/intro.md‎

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# sc2ts
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`sc2ts` (SARS-CoV-2 to tree sequence, pronounced "scoots") provides tools
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to infer and analyse tskit ancestral recombination graphs (ARGs) for SARS-CoV-2
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at pandemic scale.
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It consists of:
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1. A CLI-driven method to infer ARGs from SARS-CoV-2 data.
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2. A lightweight wrapper around the :mod:`tskit` Python APIs, specialised
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for the output of sc2ts and enabling efficient node metadata access.
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3. A lightweight wrapper around :mod:`zarr` for convenient access to the
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Viridian dataset (alignments and metadata) in VCF Zarr format.
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The underlying methods are described in the sc2ts pre-print:
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<https://www.biorxiv.org/content/10.1101/2023.06.08.544212v2>.
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Most users will run sc2ts via the command line interface,
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which drives inference and postprocessing steps (see the
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{ref}`CLI documentation <sc2ts_sec_cli>`). The Python API is intended for
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working with tree sequences and datasets produced by sc2ts (see the
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{ref}`Python API reference <api>`).
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For an overview and examples, see the project README and associated
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notebooks in the repository root.
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## Installation
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Install sc2ts from PyPI:
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```sh
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python -m pip install sc2ts
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```
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This installs the minimal requirements for the analysis and dataset APIs.
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To run inference from the command line, install the optional inference
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dependencies:
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```sh
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python -m pip install 'sc2ts[inference]'
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```
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## Quick start: ARG analysis
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To compute summary dataframes for nodes and mutations in an inferred ARG,
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you can load an sc2ts tree sequence and call the analysis helpers. For
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example, download the sc2ts paper ARG from Zenodo:
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```sh
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curl -O https://zenodo.org/records/17558489/files/sc2ts_viridian_v1.2.trees.tsz
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```
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and then:
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```python
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import sc2ts
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import tszip
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ts = tszip.load("sc2ts_viridian_v1.2.trees.tsz")
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df_node = sc2ts.node_data(ts)
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df_mutation = sc2ts.mutation_data(ts)
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```
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See the {ref}`Python API reference <api>` for full details of these
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functions.
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## Quick start: CLI inference
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To run inference locally using the example Viridian dataset and config:
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1. Install the inference extras (if you have not already):
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```sh
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python -m pip install 'sc2ts[inference]'
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```
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2. Download the Viridian dataset in VCF Zarr format:
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```sh
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curl -O https://zenodo.org/records/16314739/files/viridian_mafft_2024-10-14_v1.vcz.zip
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```
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3. Run primary inference using the CLI and the example config in this repo:
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```sh
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python -m sc2ts infer example_config.toml --stop=2020-02-02
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```
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This will produce a series of `.ts` files and a match database in the
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output directory specified by the config (see the README for details).
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4. Postprocess and generate an analysis-ready ARG:
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```sh
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python -m sc2ts postprocess -vv \
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--match-db example_inference/ex1.matches.db \
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example_inference/ex1/ex1_2020-02-01.ts \
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example_inference/ex1_2020-02-01_pp.ts
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python -m sc2ts minimise-metadata \
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-m strain sample_id \
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-m Viridian_pangolin pango \
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example_inference/ex1_2020-02-01_pp.ts \
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example_inference/ex1_2020-02-01_pp_mm.ts
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```
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The file `example_inference/ex1_2020-02-01_pp_mm.ts` can then be used
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with the Python analysis APIs shown above.
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See the {ref}`CLI documentation <sc2ts_sec_cli>` for a complete listing of
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subcommands and options.

‎docs/sc2ts.png‎

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‎pyproject.toml‎

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"matplotlib",
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"IPython",
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]
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docs = [
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"jupyter-book==1.0.4.post1",
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"sphinx-book-theme",
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"sphinx-copybutton",
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"sphinx-click",
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"sphinx-argparse==0.5.2",
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"sphinx-issues==5.0.1",
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"IPython",
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]
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[build-system]
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requires = [

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