faidx

efficient random access to fasta subsequences for Python 3

Install

All systems
curl cmd.cat/faidx.sh
Debian Debian
apt-get install python3-pyfaidx
Ubuntu
apt-get install python3-pyfaidx
image/svg+xml Kali Linux
apt-get install python3-pyfaidx
Windows (WSL2)
sudo apt-get update sudo apt-get install python3-pyfaidx
Raspbian
apt-get install python3-pyfaidx

python3-pyfaidx

efficient random access to fasta subsequences for Python 3

Samtools provides a function "faidx" (FAsta InDeX), which creates a small flat index file ".fai" allowing for fast random access to any subsequence in the indexed FASTA file, while loading a minimal amount of the file in to memory. This Python module implements pure Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index. The pyfaidx module is API compatible with the pygr seqdb module. A command-line script "faidx" is installed alongside the pyfaidx module, and facilitates complex manipulation of FASTA files without any programming knowledge. This package provides the Python 3 modules to access fasta files.