Crate segul 

Utilities for alignment manipulation and summary statistics

SEGUL provides fast and memory efficient utilities for alignment manipulation and summary statistics.

Features:

1. Alignment concatenation
2. Alignment conversion
3. Alignment filtering
4. Alignment partition conversion
5. Alignment splitting
6. Alignment summary statistics
7. Unalign alignments
8. Contiguous sequence summary statistics
9. Raw read summary statistics
10. Sample distribution mapping
11. Sequence extraction
12. Sequence filtering
13. Sequence ID renaming
14. Sequence removal
15. Sequence translation
16. Sequence unique ID parsing

Example

Convert fasta to philip alignment

use std::path::Path;

use tempdir::TempDir;

use segul::helper::types::{DataType, Header, InputFmt, OutputFmt, SeqMatrix};
use segul::helper::sequence::SeqParser;
use segul::writer::sequences::SeqWriter;

let input = Path::new("tests/files/simple.fas");
let input_fmt = InputFmt::Fasta;
let datatype = DataType::Dna;
// Replace binding with your output directory, for example:
// let output_path = Path::new("output").join("my_output_alignment");
let binding = TempDir::new("temp").unwrap();
let output_path = binding.path().join("my_output_alignment");
let output_fmt = OutputFmt::Phylip;
let (sequence_matrix, header) = SeqParser::new(input, &datatype).parse(&input_fmt);
let mut writer = SeqWriter::new(&output_path, &sequence_matrix, &header);
writer.write_sequence(&output_fmt).unwrap()

Modules

cli

Command line interface for parsing and executing commands.

core

Handle segul main functions.

helper

Helper functions for the SEGUL features.

parser

All the parsers for the supported formats.

stats

Sequence summary statistics

writer

Writer trait and its implementations.