created_at2022-12-07 13:05:40.998874
updated_at2024-03-28 08:18:25.710329
descriptionfakit: a simple program for fasta file manipulation



# fakit 🦀 a simple program for fasta file manipulation ## install latest version ```bash cargo install --git https://github.com/sharkLoc/fakit.git ``` ## install ```bash cargo install fakit ``` ## usage ```bash Fakit: A simple program for fasta file manipulation Version: 0.3.3 Authors: sharkLoc Source code: https://github.com/sharkLoc/fakit.git Fakit supports reading and writing gzip (.gz) format. Bzip2 (.bz2) and xz (.xz) format is supported since v0.3.0. Under the same compression level, xz has the highest compression ratio but consumes more time. Compression level: format range default crate gzip 1-9 6 https://crates.io/crates/flate2 bzip2 1-9 6 https://crates.io/crates/bzip2 xz 1-9 6 https://crates.io/crates/xz2 Usage: fakit [OPTIONS] Commands: topn get first N records from fasta file [aliases: head] tail get last N records from fasta file fa2fq convert fasta to fastq file faidx create index and random access to fasta files [aliases: fai] flatten flatten fasta sequences [aliases: flat] range print fasta records in a range rename rename sequence id in fasta file reverse get a reverse-complement of fasta file [aliases: rev] window stat dna fasta gc content by sliding windows [aliases: slide] grep grep fasta sequences by name/seq seq convert all bases to lower/upper case, filter by length sort sort fasta file by name/seq/gc/length search search subsequences/motifs from fasta file shuffle shuffle fasta sequences size report fasta sequence base count subfa subsample sequences from big fasta file split split fasta file by sequence id split2 split fasta file by sequence number summ simple summary for dna fasta files [aliases: stat] codon show codon table and amino acid name help Print this message or the help of the given subcommand(s) Options: -h, --help Print help -V, --version Print version Global Arguments: -w, --line-width line width when outputting fasta sequences, 0 for no wrap [default: 70] --compress-level set gzip/bzip2/xz compression level 1 (compress faster) - 9 (compress better) for gzip/bzip2/xz output file, just work with option -o/--out [default: 6] --log if file name specified, write log message to this file, or write to stderr -v, --verbosity control verbosity of logging, possible values: {error, warn, info, debug, trace} [default: debug] Global FLAGS: -q, --quiet be quiet and do not show extra information Use "fakit help [command]" for more information about a command ```
** any bugs please report issues **💖
Commit count: 0

cargo fmt