Installation

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Installation#

PyPI#

To install the fastdfe package via pip:

pip install fastdfe

fastdfe is compatible with Python 3.10 through 3.12.

Note

As of fastdfe version 1.1.12, the cyvcf2 dependency, which is required for VCF handling, is optional. To enable VCF support, install with the vcf extra:

pip install fastdfe[vcf]

Conda#

As of version 1.1.12, fastdfe is also available on conda-forge. To install it:

mamba create -n fastdfe -c conda-forge fastdfe
mamba activate fastdfe

Note

If you want to use the VCF utilities in fastdfe via conda, you also need to install cyvcf2, which is hosted on bioconda. Be sure to add the required channels:

mamba create -n fastdfe -c conda-forge -c bioconda fastdfe cyvcf2

Alternatively, to ensure reproducibility, you can create a file environment.yml:

name: fastdfe
channels:
  - conda-forge
  - bioconda
dependencies:
  - fastdfe
  - cyvcf2

Then run the following commands to create and activate the environment:

mamba env create -f environment.yml
mamba activate fastdfe

You are now ready to use fastdfe:

import fastdfe as fd
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