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. Contiguous sequence summary statistics
8. Raw read summary statistics
9. Sample distribution mapping
10. Sequence extraction
11. Sequence ID renaming
12. Sequence removal
13. Sequence translation
14. Sequence unique ID parsing

Example

Convert fasta to philip alignment

use std::path::Path;
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 output = Path::new("tests/data/alignment.phy");
let input_fmt = InputFmt::Fasta;
let output_fmt = OutputFmt::Phylip;
let datatype = DataType::Dna;

let (sequence_matrix, header) = SeqParser::new(input, &datatype).parse(&input_fmt);
let writer = SeqWriter::new(output, &sequence_matrix, &header);
writer.write_sequence(&output_fmt).unwrap()

Modules

• cli
  Command line interface for parsing and executing commands.
• handler
  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.