Features
Lightning Fast
Based on rust programming language with parallel processing and memory-mapped files for high performance.
Versatile Formats
Support for FASTA, FASTQ, GFF/GTF and other common bioinformatics formats.
Basic stable functions
Support 3 functions now: info-fetch, file-process, sequence-extract with various output formats.
Getting Started
Application
Use our Command-line App:
# Install from crates.io
cargo install seq-here
# Get basic information from sequence files
seq-here info fa sample.fasta
# Extract sequences with specific ID
seq-here extract segment sample.fasta --str GhID000001 -o output.fasta
# Extract sequences with IDs from a file
seq-here extract segment sample.fasta --file ids.txt -o output.fasta
# Extract annotated features
seq-here extract explain --seq sample.fasta --gff annotation.gff -o output_dir
# Combine multiple files
seq-here process combine file1.fasta,file2.fasta -o combined.fasta
seq-here process combine file_folder/
Lib Crate
Use our lib crate in your project:
# Add to your Cargo.toml
[dependencies]
seq-here = "0.0.5"
# Example code in your Rust project:
use seq_here::extract::ExtractSegment;
use std::path::PathBuf;
fn main() {
// Extract sequences with a specific ID
let input_files = vec![PathBuf::from("sample.fasta")];
let output_file = PathBuf::from("output.fasta");
// Extract by ID
ExtractSegment::extract_id(input_files, "SEQUENCE_ID".to_string(), output_file);
// Or process files containing annotation features
use seq_here::extract::ExtractExplain;
let seq_files = vec![PathBuf::from("sequences.fasta")];
let anno_files = vec![PathBuf::from("annotation.gff")];
let output_dir = PathBuf::from("output_directory");
ExtractExplain::extract(seq_files, anno_files, output_dir);
}
Contact Us
For any questions or suggestions, please contact us at zhixiaovo@gmail.com