seq-here

A fast tool for bio-sequence file processing.

NOTICE : This project is still under development. The current version is 0.0.4. The usage of this tool is not recommended for production yet.

Installation

You can install seq-here using cargo:

cargo install seq-here

or you can build it from source:

git clone git@github.com:bio-here/seq-here.git
cd seq-here
cargo build --release
cp target/release/seq-here /usr/local/bin

seq-here --version

Lib Crate

You can also use seq-here as a library crate in your project, by adding the following to your Cargo.toml:

[dependencies]
seq-here = "0.0.4"

Usage

To see detailed usage information, you can run:

seq-here --help

• Info: Get basic information about the input sequence file(s).

# Fasta file information
seq-here info fa you_files.fasta,your_files2.fasta

# Fastq file information
seq-here info fq your_files.fastq

# Gff/Gtf file information, Gff2 not supported yet
seq-here info gff your_files.gff

# -o, --output: output method, default is println
# 3 options: println, file, csv
# The file will be put in the current directory
seq-here info fa your_files.fasta -o file

# input a directory to get all files information below the directory
seq-here info fa your_dir

• Process: Convert or process incoming sequence file(s).

# Combine files
seq-here process combine files_folder

# -o, --output <OutputFile>
#         Output file name, if value is a directory, it would use default file_name in the directory.


seq-here process combine files_folder -o ./output/all.txt

• Extract: Extract specified sequence segment or file data.

seq-here extract segment

seq-here extract 

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

License

This project is licensed under the MIT License - see the LICENSE file for details.