FastaTools

This is a simple command line utility to deal with FASTA formatted biological sequence collections, inspired by goalign and built in with bashly.

The idea is to have very simple operations (mainly using awk) so they can be executed on a per sequence basis, eliminating the need to load the whole file in memory. This allows the user to operate on very large FASTA files.

Installation

This tool is distributed as a shell script. So if you download the fastatools script it should work seamlessly on *NIX systems.

Documentation

For now you can refer to the generated help message by using fastatools help or fastatools [command] help or the definition file.

This is designed to be pipeable, so the default IO is standard input and output. However for all commands the -ior --input flag can be used to specify an input and for most commands the -o or --output flag can be used to specify an output flag.

List of commands

This is a short list presenting the avaiable fastatools commands.

Information commands

• count: Get the number of sequences
• names: Get names of sequences
• length: Get lengths of sequences
• freqs: Get character frequencies in sequences

Selection commands

• select: Select sequences in FASTA file by name
• subset: Select sequences in FASTA file by index
• head: Print first n sequences
• tail: Print last n sequences
• subsite: Select specific sites in aligned sequences

Transformation commands

• upper: Transform sequences to uppercase
• lower: Transform sequences to lowercase
• pretty: Pretty print FASTA file, wrapping sequences to desired width
• rc: Reverse complement sequences

Name manipulation commands

• rename: Rename sequences in FASTA file
• addid: Add an identified to each sequence name in a sequence name

Splitting commands

• split: Split a fasta file into several fasta files

Others

• completion: Generate BASH completion script (auto-generated by bashly)