Expand description
!
This crate provides several functions for bio-sequence file processing. It is designed to be fast and easy to use.
Use the crate in your project by adding the following to your Cargo.toml:
seq-here = "0.1.0"There are 3 modules in this crate for different purposes:
- info: Get basic information about the input sequence file(s).
- process: Process incoming sequence file(s).
- extract: Extract specified sequence segment or file data.
§Examples
- Info module:
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:
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:
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);