12 releases
0.3.8 | Jun 17, 2024 |
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0.3.6 | May 20, 2024 |
0.3.3 | Mar 28, 2024 |
0.2.9 | Nov 21, 2023 |
0.2.0 |
|
#79 in Biology
29 downloads per month
88KB
2.5K
SLoC
fakit
🦀 a simple program for fasta file manipulation
install latest version
cargo install --git https://github.com/sharkLoc/fakit.git
install
cargo install fakit
usage
Fakit: A simple program for fasta file manipulation
Version: 0.3.8
Authors: sharkLoc <mmtinfo@163.com>
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] <COMMAND>
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
kmer a simple kmer counter
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)
Global Arguments:
-w, --line-width <int> line width when outputting fasta sequences, 0 for no wrap [default: 70]
--compress-level <int> 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 <str> if file name specified, write log message to this file, or write to stderr
-v, --verbosity... control verbosity of logging, [-v: Error, -vv: Warn, -vvv: Info, -vvvv: Debug, -vvvvv: Trace, defalut: Debug]
Global FLAGS:
-q, --quiet be quiet and do not show extra information
-h, --help prints help information
-V, --version prints version information
Use "fakit help [command]" for more information about a command
** any bugs please report issues **💖
Dependencies
~29–42MB
~704K SLoC