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update REAME.md for v0.2 (#240)
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Removes outdated references to v0.1

Adds additional information for installation of v0.2 using conda,
pip, and from downloaded source code. Hopefully this is clearer.

Adds a more strident notice about the relationship between 0.2 and
0.3 (0.2 maintenance-only; default repo is 0.3; etc.)

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widdowquinn committed Mar 10, 2021
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159 changes: 94 additions & 65 deletions README_v_0_2_x.md
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<!-- TOC -->

- [Overview](#overview)
- [Installation](#installation)
- [Docker images](#docker-images)
- [Testing `pyani`](#testing-pyani)
- [Running `pyani`](#running-pyani)
- [README.md (pyani)](#readmemd-pyani)
- [Overview](#overview)
- [Installation](#installation)
- [`conda`](#conda)
- [`pip`](#pip)
- [Docker images](#docker-images)
- [NOTE](#note)
- [Installing from the repository/source code](#installing-from-the-repositorysource-code)
- [IMPORTANT NOTICE](#important-notice)
- [Direct download](#direct-download)
- [Clone the repository using `git`](#clone-the-repository-using-git)
- [Installation](#installation-1)
- [Third-party tools](#third-party-tools)
- [Testing `pyani`](#testing-pyani)
- [Running `pyani`](#running-pyani)
- [Script: `average_nucleotide_identity.py`](#script-average_nucleotide_identitypy)
- [Script: `genbank_get_genomes_by_taxon.py`](#script-genbank_get_genomes_by_taxonpy)
- [DEPENDENCIES](#dependencies)
- [For ANI analysis](#for-ani-analysis)
- [For graphical output](#for-graphical-output)
- [Method and Output Description](#method-and-output-description)
- [Method and Output Description](#method-and-output-description)
- [Average Nucleotide Identity (ANI)](#average-nucleotide-identity-ani)
- [Developer notes](#developer-notes)
- [Code Style and Pre-Commit Hooks](#code-style-and-pre-commit-hooks)
- [Licensing](#licensing)
- [Licensing](#licensing)

<!-- /TOC -->

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## Installation

The easiest way to install `pyani` is to use `pip3`:
The easiest way to install `pyani` v0.2 is to use `conda` or `pip`. `conda` is recommended for the simplest installation of third-party tool dependencies (`mummer` and `BLAST`/`BLAST+`).

### `conda`

You will need to install the `bioconda` channel, following instructions at [https://bioconda.github.io/user/install.html](https://bioconda.github.io/user/install.html).

```bash
pip3 install pyani
conda create --name pyani_env python=3.8 -y
conda activate pyani_env
conda install mummer blast legacy-blast -y
conda install pyani
```

From version 0.1.3.2 onwards, this should also install all the required Python package dependencies. Prior to this version (i.e. 0.1.3.1 and earlier), you can acquire these dependencies with `pip -r`, and pointing at `requirements.txt` from this repository:
### `pip`

`pip` will install `pyani` and its Python dependencies, but not the third-party tools.

```bash
pip3 install -r requirements.txt
pip3 install pyani
```

## Docker images

`pyani`'s scripts are also provided as [Docker](https://www.docker.com/) images, that can be run locally as containers. To use these images, first install Docker, then to run the corresponding scripts issue either:
`pyani` v0.2 scripts are also provided as [Docker](https://www.docker.com/) images, that can be run locally as containers. To use these images, first install Docker. Then, to run the corresponding scripts, issue either:

```bash
docker run -v ${PWD}:/host_dir leightonpritchard/average_nucleotide_identity
Expand All @@ -64,17 +78,74 @@ or
docker run -v ${PWD}:/host_dir leightonpritchard/genbank_get_genomes_by_taxon
```

### NOTE

The `-v ${PWD}:/host_dir` argument enables the Docker container to see the current directory. Without this argument, the container will not be able to see your input files, or write output data.

## Testing `pyani`
## Installing from the repository/source code

If you wish to install `pyani` v0.2 from source code, you will need to download this code from GitHub either directly, or by cloning the repository.

Both methods will create a directory called `pyani` which contains the source code for v0.2.

### IMPORTANT NOTICE

**THE DEFAULT REPOSITORY ON `GITHUB` IS `PYANI` v0.3+, *NOT* v0.2. THE INSTRUCTIONS ON THE MAIN REPOSITORY `README.md` DO NOT APPLY TO v0.2**

Please note that v0.2 is a **MAINTENANCE-ONLY RELEASE**. This means that bugs and security issues will be fixed, but no new features will be added. All new feature development now takes place under v0.3 (the `master` branch on the repository).

### Direct download

Download the source as `.zip` or `.tar.gz` from [https://github.com/widdowquinn/pyani/releases/tag/v0.2.10](https://github.com/widdowquinn/pyani/releases/tag/v0.2.10)

Extract the archived file using the appropriate commands (or by double-clicking in your file explorer/finder):

```bash
unzip v0.2.10.zip
```

or

```bash
tar -zxvf v0.2.10.tar.gz
```

### Clone the repository using `git`

Download the current `pyani` repository with `git clone`, and change branch to `version_0_2`:

```bash
git clone git@github.com:widdowquinn/pyani.git
git checkout version_0_2
```

`pyani` includes tests that can be run with `nosetest` (including coverage measurement using `coverage.py`) with the following command, executed from the repository root directory:
### Installation

Change directory to `pyani`, and use the `python setup.py` setuptools command, to install the package and scripts. This will **not** install the third-party tools `BLAST`/`BLAST+` and `mummer`.

```bash
nosetests --cover-erase --cover-package=pyani --cover-html --with-coverage
cd pyani
python setup.py build
python setup.py install
```

Coverage output will be placed (by default) in the `cover` subdirectory, and can be loaded into the web browser.
### Third-party tools

Three alignment packages are required, to use all of `pyani`'s methods: `mummer`, `BLAST+`, and legacy `BLAST`.

The simplest route to obtaining these tools is to use `conda`/`bioconda`. But they can be installed by following instructions from the tools' own websites.

- **BLAST+** (for `anib`) [ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
- **legacy BLAST** (for `aniblastall`) [ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/)
- **MUMmer** (for `anim`) [http://mummer.sourceforge.net/](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/)

## Testing `pyani`

The `pyani` repository includes tests that can be run with `pytest` (including coverage measurement using `pytest-cov) with the following command, executed from the repository root directory:

```bash
pytest -v
```

## Running `pyani`

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The number of attempted retries for each download, and the size of a batch download can be modified. By default, the script will attempt 20 download retries, and obtain sequences in batches of 10000.

## DEPENDENCIES

Note that Python package dependencies should automatically be installed if you are using version 0.1.3.2 or greater, and installing with `pip install pyani`.

For earlier versions, you can satisfy dependencies by using `pip install -r requirements.txt` (using the `requirements.txt` file in this repository).

### For ANI analysis

- **Biopython** <http://www.biopython.org>
- **NumPy** <http://www.numpy.org/>
- **pandas** <http://pandas.pydata.org/>
- **SciPy** <http://www.scipy.org/>

#### Alignment tools

- **BLAST+** executable in the `$PATH`, or available on the command line (required for **ANIb** analysis) <ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/>
- **legacy BLAST** executable in the `$PATH` or available on the command line (required for **ANIblastall** analysis) <ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/>
- **MUMmer** executables in the $PATH, or available on the command line (required for **ANIm** analysis) <http://mummer.sourceforge.net/>

### For graphical output

- **matplotlib** <http://matplotlib.org/>
- **seaborn** <https://github.com/mwaskom/seaborn>

## Method and Output Description

### Average Nucleotide Identity (ANI)
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If graphical output is chosen, the output directory will also contain PDF, PNG and EPS files representing the various output measures as a heatmap with row and column dendrograms. Other output formats (e.g. SVG) can be specified with the `--gformat` argument.

## Developer notes

The `pyani` package is presented at [`GitHub`](https://github.com/widdowquinn/pyani) under two main branches:

- `master` is the source code underpinning the most recent/current release of `pyani`. It will (almost) always be in sync with the latest release found at [https://github.com/widdowquinn/pyani/releases](https://github.com/widdowquinn/pyani/releases). The only time this code should not be in sync with the release is when there are modifications to documentation, or immediately preceding a release.
- `development` is the current bleeding-edge version of `pyani`. It should (almost) always be in a working and usable condition, but may not be complete and/or some features may be missing or still under development.

### Code Style and Pre-Commit Hooks

The source code for `pyani` is expected to conform to `flake8` linting, and `black` code styling. These are enforced as pre-commit hooks using the `pre-commit` package (included in `requirements.txt`).

The `black` and `flake8` hooks are defined in `.pre-commit-config.yaml`. Custom settings for `flake8` are held in `.flake8`.

To enable pre-commit checks in the codebase on your local machine, execute the following command in the root directory of this repository:

```bash
pre-commit install
```

## Licensing

Unless otherwise indicated, all code is subject to the following agreement:

>(c) The James Hutton Institute 2014-2019
>(c) The University of Strathclyde 2019
>(c) The University of Strathclyde 2019-2021
>Author: Leighton Pritchard
>
>Contact: leighton.pritchard@strath.ac.uk
Expand All @@ -276,7 +305,7 @@ Unless otherwise indicated, all code is subject to the following agreement:
>The MIT License
>
>Copyright (c) 2014-2019 The James Hutton Institute
>Copyright (c) 2019 The University of Strathclyde
>Copyright (c) 2019-2021 The University of Strathclyde
>
>Permission is hereby granted, free of charge, to any person obtaining a copy
>of this software and associated documentation files (the "Software"), to deal
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