Encoding Suffix Trees

AUTHOR

L. Grondin

http://rosalind.info/problems/suff/

Sample input

ATAAATG$

Sample output

AAATG$
    G$
    T
    ATG$
    TG$
    A
    A
    AAATG$
    G$
    T
    G$
    $
use v6;



sub suffixes(Str $str) { map *.flip, [\~] $str.flip.comb }
sub suffix-tree(@a) {
    @a == 0 ?? [] !!
    @a == 1 ?? hash @a[0] => [] !!
    hash gather for @a.classify(*.substr(0, 1)) {
        my $subtree = suffix-tree([ grep *.chars, map *.substr(1), .value[] ]);
        if $subtree.elems == 1 {
            my $pair = $subtree.pick;
            take .key ~ $pair.key => $pair.value;
        } else {
            take .key => $subtree;
        }
    }
}

sub show-edges($tree) {
    return if $tree.elems == 0;
    for $tree[] {
        say .key;
        show-edges .value;
    }
}

sub MAIN(Str $input = 'ATAAATG$') {
    show-edges suffix-tree suffixes $input;
}

# vim: expandtab shiftwidth=4 ft=perl6

See Also

afrq-grondilu.raku

Counting Disease Carriers

aspc-grondilu.raku

Introduction to Alternative Splicing

cons-grondilu.raku

Consensus and Profile

conv-grondilu.raku

Comparing Spectra with the Spectral Convolution

cstr-grondilu.raku

Creating a Character Table from Genetic Strings

ctbl-grondilu.raku

Creating a Character Table

dbpr-grondilu.raku

Introduction to Protein Databases

dna-gerdr.raku

Counting DNA Nucleotides

dna-grondilu.raku

Counting DNA Nucleotides

eubt-grondilu.raku

Enumerating Unrooted Binary Trees

eval-grondilu.raku

Expected Number of Restriction Sites

fib-grondilu.raku

Rabbits and Recurrence Relations

fibd-grondilu.raku

Mortal Fibonacci Rabbits

gc-gerdr.raku

Computing GC Content

grph-grondilu.raku

Overlap Graphs

hamm-grondilu.raku

Counting Point Mutations

iev-grondilu.raku

Calculating Expected Offspring

indc-grondilu.raku

Independent Segregation of Chromosomes

iprb-grondilu.raku

Mendel's First Law

itwv-grondilu.raku

Finding Disjoint Motifs in a Gene

lcsq-grondilu.raku

Finding a Shared Spliced Motif

lia-grondilu.raku

Independent Alleles

lrep-grondilu-p5.raku

mmch-grondilu.raku

Maximum Matchings and RNA Secondary Structures

mprt-grondilu.raku

Finding a Protein Motif

mrna-grondilu.raku

Inferring mRNA from Protein

nwck-grondilu.raku

Distances in Trees

orf-grondilu.raku

Open Reading Frames

pmch-grondilu.raku

Perfect Matchings and RNA Secondary Structures

pper-grondilu.raku

Partial Permutations

prob-grondilu.raku

Introduction to Random Strings

qrt-grondilu.raku

Quartets

README.md

revc-gerdr.raku

Complementing a Strand of DNA

rna-gerdr.raku

Transcribing DNA into RNA

rstr-grondilu.raku

Matching Random Motifs

sexl-grondilu.raku

Sex-Linked Inheritance

sgra-grondilu.raku

Using the Spectrum Graph to Infer Peptides

spec-grondilu.raku

Inferring Protein from Spectrum

sseq-grondilu.raku

Finding a Spliced Motif

subs-grondilu.raku

Finding a Motif in DNA

tran-grondilu.raku

Transitions and Transversions

trie-grondilu.raku

Introduction to Pattern Matching

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