Crate segul_core 

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 pairwise genetic distances
5. Alignment partition conversion
6. Alignment splitting
7. Alignment summary statistics
8. Unalign alignments
9. Contiguous sequence summary statistics
10. Raw read summary statistics
11. Sample distribution mapping
12. Sequence extraction
13. Sequence filtering
14. Sequence ID renaming
15. Sequence removal
16. Sequence translation
17. Sequence transposition
18. Sequence unique ID parsing

Cargo features

All features are enabled by default. Disable default features and pick the ones you need to reduce compile time and dependencies:

Feature	Provides
align	Alignment concat, convert, distance, filter, split, summary, trim
sequence	Sequence extract, filter, rename, remove, translate, transpose, ID
read	Raw read (FASTQ) summary statistics
contig	Contiguous sequence summary statistics
maf	Multiple alignment format (MAF) conversion

segul-core = { version = "0.24", default-features = false, features = ["read"] }

Example

Convert fasta to philip alignment

use std::path::Path;

use tempfile::TempDir;

use segul_core::helper::types::{DataType, Header, InputFmt, OutputFmt, SeqMatrix};
use segul_core::helper::sequence::SeqParser;
use segul_core::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::with_prefix("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

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.