seq-here😼

seq-here is a fast tool for bio-sequence file processing.

seq-here provides multiple functions for bio-sequence file processing, including obtaining basic information, processing sequence files, and extracting specific sequence segments.

Installation

You can install seq-here using cargo:

cargo install seq-here

If you haven't installed the Rust toolchain, you can also download our pre-compiled binary files directly from GitHub Release:

• Release

TIP

We have pre-compiled programs for Windows and Linux amd64 versions. If you want to use placecare on other platforms, the best approach is to install it through the Rust toolchain.

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

Library Integration

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

[dependencies]
seq-here = "0.1.0"

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 your_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
seq-here process combine file1,file2,file3

# -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

# Extract a sequence segment by id
seq-here extract segment input.fasta --file sequence_id.txt
seq-here extract segment input.fasta --str GhID00000001

# Extract a specific portion of a sequence by position (0-based coordinates)
seq-here extract segment input.fasta --str GhID00000001 --start 100 --end 200
seq-here extract segment input.fasta --file ids.txt --start 50 --end 150

# Extract sequences by given annotation file
seq-here extract explain --seq input.fasta --gff input.anno.gff -o output_path.fasta

# Extract only specific feature types from annotations
seq-here extract explain --seq input.fasta --gff input.anno.gff --type CDS,gene,mRNA -o output_path

Library Functions

There are 3 modules in seq-here for different purposes:

1. info: Get basic information about the input sequence file(s)
2. process: Process incoming sequence file(s)
3. extract: Extract specified sequence segment or file data

Info Module Example

use seq_here::info::{self, InfoOutput};
use std::path::{Path, PathBuf};

let paths = vec![PathBuf::from("tests/test.fa")];
info::InfoFa::by_println(paths.clone());
info::InfoFa::by_file(paths);

Process Module Example

use seq_here::process::{self};
use std::path::PathBuf;

// Combine multiple files into one
let input_files = vec![PathBuf::from("file1.txt"), PathBuf::from("file2.txt")];
let output_file = PathBuf::from("combined.txt");
seq_here::process::ConvertCombine::combine_all(input_files, output_file);

Extract Module Example

use seq_here::extract::{ExtractSegment, ExtractExplain};
use std::path::PathBuf;

// Extract sequence by ID
let input_files = vec![PathBuf::from("sequence.fasta")];
let output_file = PathBuf::from("extracted.fasta");
let id = "sequence_id".to_string();

// Extract full sequence matching the ID
ExtractSegment::extract_id(input_files.clone(), id.clone(), output_file.clone(), None, None);

// Extract a specific segment (positions 10 to 50) from the sequence
ExtractSegment::extract_id(input_files, id, output_file, Some(10), Some(50));

// Extract features from annotation files
let seq_files = vec![PathBuf::from("genome.fasta")];
let anno_files = vec![PathBuf::from("annotations.gff")];
let output_dir = PathBuf::from("extracted_features");

// Extract all annotated features
ExtractExplain::extract(seq_files.clone(), anno_files.clone(), output_dir.clone(), None);

// Extract only CDS and gene features
let feature_types = Some(vec!["CDS".to_string(), "gene".to_string()]);
ExtractExplain::extract(seq_files, anno_files, output_dir, feature_types);

Tips

Citation

If your article uses this software, it means you used the libraries used by this software, please cite the following articles:

• Rust-Bio

Köster, J. (2016). Rust-Bio: a fast and safe bioinformatics library. Bioinformatics, 32(3), 444-446.