My (Max's?) Minimal Fasta Toolkit

Nothing sophisticated. Minimal, simple fasta tools.

It's stuff that's been done many times, but this way I can get it just the way I like it. May be of use to others.

Usage

Calculations

• mmft len or cat | mmft len . Calculates lengths of each fasta record.
• mmft gc or cat | mmft gc . Calculates GC content of each fasta record.
• mmft n50 or cat | mmft n50 . Calculates n50 of a fasta record (or stream of fasta files combined).
• mmft num or cat | mmft num . Calculates number of sequences, and total number of base pairs in the fasta file input(s).

File manipulations

• mmft regex -r " " or cat | mmft regex -r " " . Extracts fasta records from one or multiple fasta files with headers matching the regex.
• mmft extract -r 1-100 or cat | mmft extract -r 1-100 . Extracts first 100 nucleotides from each fasta record. You can of course choose any range, using a dash to separate the numbers.

Careful when piping into mmft as fasta files are not treated separately, they are treated as a continuum of fasta records. Hence, while mmft n50 1.fasta 2.fasta shows the n50 of each fasta file separately, cat *.fasta | mmft n50 will calculate the n50 of both files combined.

All printed to STDOUT.

TODO's

I'll add stuff as and when I have time, or they are of use. Maybe:

• Simple pattern matching, returning positions.
• Potential ORFs
• Any kmer stuff?

Motivation

Interesting to explore the thiserror and the anyhow crates in the making of this repo.