LtFmIndex
lt-fm-index
is library for locate and count nucleotide and amino acid sequence string.
Description
- Fm-index is a data structure for exact pattern matching.
- LtFmIndex have precalculated count lookup table for kmer occurrences.
- The lookup table can locate first k-mer pattern at once.
Features
LtFmIndex
is generated fromText
LtFmIndex
have two functions forPattern
- count: Count the number of times the
Pattern
appears inText
. - locate: Locate the start index in which the
Pattern
appears inText
.
- count: Count the number of times the
- Supports four types of text.
NucleotideOnly
: ACGTNucleotideWithNoise
: ACGT_AminoacidOnly
: ACDEFGHIKLMNPQRSTVWYAminoacidWithNoise
: ACDEFGHIKLMNPQRSTVWY_
- The last character of each text type (T, _, Y, _) is treated as a wildcard that can be assigned to all non-supported characters.
- For example, in
NucleotideOnly
, pattern of ACGTXYZ can be matched with ACGTTTT. Because X, Y and Z are not in ACG (nucleotide except T). Andlt-fm-index
generated with text of ACGTXYZ indexes the text as ACGTTTT.
- For example, in
Examples
1. Use LtFmIndex
to count and locate pattern.
use LtFmIndexBuilder;
// (1) Define builder for lt-fm-index
let builder = new
.use_nucleotide_with_noise
.set_lookup_table_kmer_size.unwrap
.set_suffix_array_sampling_ratio.unwrap;
// (2) Generate lt-fm-index with text
let text = b"CTCCGTACACCTGTTTCGTATCGGANNNN".to_vec;
let lt_fm_index = builder.build; // text is consumed
// (3) Match with pattern
let pattern = b"TA".to_vec;
// - count
let count = lt_fm_index.count;
assert_eq!;
// - locate
let locations = lt_fm_index.locate;
assert_eq!;
2. Save and load LtFmIndex
use ;
// (1) Generate lt-fm-index
let text = b"CTCCGTACACCTGTTTCGTATCGGA".to_vec;
let lt_fm_index_to_save = new.build;
// (2) Save lt-fm-index to buffer
let mut buffer = Vec new;
lt_fm_index_to_save.save_to.unwrap;
// (3) Load lt-fm-index from buffer
let lt_fm_index_loaded = load_from.unwrap;
assert_eq!;
Repository
https://github.com/baku4/lt-fm-index
Doc
Reference
- Ferragina, P., et al. (2004). An Alphabet-Friendly FM-Index, Springer Berlin Heidelberg: 150-160.
- Anderson, T. and T. J. Wheeler (2021). An optimized FM-index library for nucleotide and amino acid search, Cold Spring Harbor Laboratory.
- Wang, Y., X. Li, D. Zang, G. Tan and N. Sun (2018). Accelerating FM-index Search for Genomic Data Processing, ACM.
- Yuta Mori.
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