Installation

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Installation#

PyPi#

To install the fastdfe package, you can use pip:

pip install fastdfe

fastdfe is compatible with Python 3.10 through 3.12.

Note

Support for VCF input (e.g., reading .vcf.gz files) in fastdfe requires the optional cyvcf2 dependency. To enable this functionality, install with the vcf extra:

pip install fastdfe[vcf]

Conda#

To avoid potential conflicts with other packages, it is recommended to install fastdfe in an isolated environment. The easiest way to do this is to use conda (or mamba):

To do this, run:

mamba create -n fastdfe 'python>=3.10,<3.13' pip
mamba activate fastdfe
pip install fastdfe

Alternatively, create a new file called environment.yml with the following content:

name: fastdfe
channels:
  - defaults
dependencies:
  - python>=3.10,<3.13
  - pip
  - pip:
      - fastdfe

Then run the following command to create the environment:

mamba env create -f environment.yml

Activate the newly created environment:

mamba activate fastdfe

You are now ready to use the fastdfe package within the isolated conda environment.

import fastdfe as fd
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