Metadata-Version: 2.4
Name: dark-matter
Version: 7.0.1
Summary: Python library and utility scripts for working with genetic sequence data.
Author: Barbara Mühlemann, Tali Veith, Sophie Mathias, Udo Gieraths, Nikolai Zaki, David Pattinson
Author-email: Terry Jones <tcj25@cam.ac.uk>
License-Expression: MIT
Project-URL: Homepage, https://github.com/acorg/dark-matter
Project-URL: Bug Tracker, https://github.com/acorg/dark-matter/issues
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: <3.14,>=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
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Dynamic: license-file

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## Dark matter

A collection of Python tools for filtering and visualizing
[Next Generation Sequencing](https://en.wikipedia.org/wiki/DNA_sequencing#Next-generation_methods)
reads.

## Installation

On Linux (at least) you will need to first:

```sh
sudo apt install zlib1g-dev libbz2-dev liblzma-dev
```

Then you should be able to install via

```sh
$ pip install dark-matter
```

Some additional information is available for
[Linux](doc/linux.md), [OS X](doc/mac.md), and [Windows](doc/windows.md).

## Optional dependencies

Not all of the following are mandatory. It depends which part of the
dark-matter code you try to use.

### Picard

`run-bowtie2.py` can use [Picard](https://broadinstitute.github.io/picard/)
to mark duplicates.

### GATK

`run-bowtie2.py` uses [gatk](https://gatk.broadinstitute.org) if you call
it with `--markDuplicatesGATK` or `--callHaplotypesGATK`. If you want to do
this you'll need to download the `gatk` zip file, unzip it, and either put
the directory where you unzip it into your shell's path or else move the
contents of the zip file into a directory already in your path.

### bcftools

You'll need
[bcftools](http://samtools.github.io/bcftools/howtos/index.html) if you
want to make consensuses using the `make-consensus.py` script. Either
follow
[the installation instructions](http://samtools.github.io/bcftools/howtos/install.html)
or, if you use [brew](https://brew.sh/) (or Linux brew), `brew install bcftools`.

### samtools

The `run-bowtie2.py` and `run-bwa.py` scripts both make use of
[samtools](https://www.htslib.org/).

### EMBOSS

The `compare-sequences.py` script (if called with `--align`) requires the
`needle` and (possibly) `stretcher` from
[EMBOSS](http://emboss.sourceforge.net/).

### iPython Notebook

If you are using dark matter in an
[iPython Notebook](https://ipython.org/notebook.html), you should install
the requirements in `requirements-ipynb.txt`.

## Development

If you are using dark matter as a developer, you should install the
requirements in `requirements-dev.txt`.
