better-fasta-grep

Better FASTA Grep

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.

Features

• 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.

Quick installation

The easiest way to install this program is via pip:

pip install better_fasta_grep

You can then launch bfg using one of the following commands:

bfg --help
better_fasta_grep --help # equivalent

Documentation

1. Introduction
2. Installation
3. Invoking bfg
4. Regular Expressions
5. Input Data
6. Usage

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