faidx
efficient random access to fasta subsequences for Python 3
Install
- All systems
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curl cmd.cat/faidx.sh
- Debian
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apt-get install python3-pyfaidx - Ubuntu
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apt-get install python3-pyfaidx - Kali Linux
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apt-get install python3-pyfaidx - Windows (WSL2)
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sudo apt-get updatesudo apt-get install python3-pyfaidx - Raspbian
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apt-get install python3-pyfaidx - Dockerfile
- dockerfile.run/faidx
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.