Better FASTA Grep, or BFG for short, is a Grep-like utility for retrieving matching sequence records from a FASTA file. Given one or more patterns and a FASTA file, it searches the file for matching headers and or sequences and outputs any matching headers, sequences, or both.
- Search headers, sequences, or both
- Search via regular expressions or plain strings
- Case-insensitive search
- Select non-matching sequence records
- Count the number of matches
- Display line numbers in the result
- Sequence records, not individual lines, are selected
- Multi-line sequences are treated as singular units
- Flexible output options: output headers, sequences, or both
A screenshot of running BFG under macOS Mojave.
The easiest way to install this program is via pip:
pip install better_fasta_grepYou can then launch bfg using one of the following commands:
bfg --help
better_fasta_grep --help # equivalent© Department for Animal Evolution and Biodiversity 2019