https://github.com/moold/fxtools
A toolset for processing sequences in FASTA/Q formats
https://github.com/moold/fxtools
Last synced: about 1 year ago
JSON representation
A toolset for processing sequences in FASTA/Q formats
- Host: GitHub
- URL: https://github.com/moold/fxtools
- Owner: moold
- License: gpl-3.0
- Created: 2021-08-09T14:06:37.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2025-04-10T03:19:46.000Z (about 1 year ago)
- Last Synced: 2025-04-10T04:26:38.596Z (about 1 year ago)
- Language: Rust
- Homepage:
- Size: 99.6 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# fxTools
A toolset for processing sequences in FASTA/Q formats
## Installation
#### Dependencies
`fxTools` is written in rust, see [here](https://www.rust-lang.org/tools/install) to install `Rust` first.
#### Download and install
```sh
git clone git@github.com:moold/fxTools.git
cd fxTools && cargo build --release
# ./target/release/fxTools
```
## Usage and Parameters
```
fxTools
A toolset for processing sequences in FASTA/Q formats
USAGE:
fxTools [SUBCOMMAND] [OPTIONS] ...
ARGS:
... input file ...
OPTIONS:
-a, --attr get sequence attributes, id:len:x:qs
len: sequences length
x: count x, case sensitive, where x can be a single base
or multiple bases (gcGC means count g + c + G + C)
qs: quality score, for FASTQ
-r, --reform reform/modify the sequence, accept values:
lower: convert sequences into lowercase
upper: convert sequences into uppercase
fq2fa: converts FASTQ to FASTA
fa2fq: converts FASTA to FASTQ
rev: reverse the sequence
com: complement the sequence
rc: reverse and complement the sequence
lineINT[c]:
wrap sequences into INT characters per line,
0 for no wrap, c is the alignment mode,
color for SNVs and INDELs
linkINT: link sequences with INT Ns
-p, --split split file with INT subfiles in total
-s, --sample subsample reads, int is the total bases, float is the
fraction
-h, --help Print help information
-V, --version Print version information
SUBCOMMANDS:
stat simple statistics of FASTA/Q files
findseq find subseq positions
findgap find gap(Nn) regions
getseq get sequences or subsequences from a region or file
diff compare sequences between two files
```