Crate segul

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§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.
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.