rosalind

罗莎琳德问题解决方案库

API 文档

lib.rs:

rosalind 提供了解决来自 Rosalind 网站问题的函数。

计算 DNA 核苷酸

示例

use rosalind::RosalindError::UnknownNucleotide;
use rosalind::dna::*;

let dna = "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC";
let dna_nucleotides = DNANucleotides {A: 20, C: 12, G: 17, T: 21};
assert_eq!(count_dna_nucleotides(dna).unwrap(), dna_nucleotides);
assert_eq!(dna_nucleotides.to_string(), "20 12 17 21");
assert_eq!(count_dna_nucleotides("\n").unwrap(), DNANucleotides {A: 0, C: 0, G: 0, T: 0});
assert_eq!(count_dna_nucleotides("Z").unwrap_err(), UnknownNucleotide('Z'));

将 DNA 转录为 RNA

示例

use rosalind::RosalindError::UnknownNucleotide;
use rosalind::rna::*;

let dna = "GATGGAACTTGACTACGTAAATT";
assert_eq!(transcribe_dna_into_rna(dna).unwrap(), "GAUGGAACUUGACUACGUAAAUU");
assert_eq!(transcribe_dna_into_rna("\n").unwrap(), "");
assert_eq!(transcribe_dna_into_rna("Z").unwrap_err(), UnknownNucleotide('Z'));

互补 DNA 链

示例

use rosalind::RosalindError::UnknownNucleotide;
use rosalind::revc::*;

let dna = "AAAACCCGGT";
assert_eq!(reverse_complement_dna(dna).unwrap(), "ACCGGGTTTT");
assert_eq!(reverse_complement_dna("\n").unwrap(), "");
assert_eq!(reverse_complement_dna("Z").unwrap_err(), UnknownNucleotide('Z'));

兔子与递归关系

示例

use rosalind::fib::*;
use num::{BigUint};
use num::bigint::{ToBigUint};

let mut expected_relation: BigUint = 19.to_biguint().unwrap();
assert_eq!(recurrence_relation(5, 3).unwrap(), expected_relation);
expected_relation = 4.to_biguint().unwrap();
assert_eq!(recurrence_relation_with_stop(6, 3).unwrap(), expected_relation);

将 RNA 转译为蛋白质，推断 mRNA 从蛋白质，计算蛋白质质量

示例

use rosalind::RosalindError::{CodonParseError, UnknownCodon, UnknownAminoAcid};
use rosalind::prot::*;

let rna = "AUGGCCAUGGCGCCCAGAACUGAGAUCAAUAGUACCCGUAUUAACGGGUGA";
assert_eq!(translate_rna_into_protein(rna).unwrap(), "MAMAPRTEINSTRING");
assert_eq!(translate_rna_into_protein("AUGUGA\n").unwrap(), "M");
assert_eq!(translate_rna_into_protein("Z").unwrap_err(), CodonParseError);
assert_eq!(translate_rna_into_protein("ZZZ").unwrap_err(), UnknownCodon("ZZZ".to_string()));

assert_eq!(get_number_of_rna_from_protein("MA").unwrap(), 12);
assert_eq!(get_number_of_rna_from_protein("").unwrap(), 0);
assert_eq!(get_number_of_rna_from_protein("\n").unwrap(), 3);
assert_eq!(get_number_of_rna_from_protein("B").unwrap_err(), UnknownAminoAcid('B'));

assert_eq!(get_protein_mass("SKADYEK\n").unwrap(), 821.392f64);
assert_eq!(get_protein_mass("AB").unwrap_err(), UnknownAminoAcid('B'));

计算点突变

示例

use rosalind::RosalindError::HammingStringsLengthError;
use rosalind::hamm::*;

let s = "GAGCCTACTAACGGGAT";
let t = "CATCGTAATGACGGCCT";
assert_eq!(hamming_distance(s, t).unwrap(), 7);
assert_eq!(hamming_distance("G", "").unwrap_err(), HammingStringsLengthError);

在 DNA 中找到基序

示例

use rosalind::RosalindError::MotifStringsLengthError;
use rosalind::subs::*;

let s = "GATATATGCATATACTT";
let t = "ATAT";
assert_eq!(motif_lookup(s, t).unwrap(), vec![2, 4, 10]);
assert_eq!(motif_lookup(t, s).unwrap_err(), MotifStringsLengthError);

计算 GC 含量

示例

use rosalind::gc::*;

assert_eq!(gc_content("").unwrap(), 0f32);
assert_eq!(gc_content("AGCTATAG").unwrap(), 37.5f32);

let dataset = ">Rosalind_6404
  CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
  TCCCACTAATAATTCTGAGG
  >Rosalind_5959
  CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
  ATATCCATTTGTCAGCAGACACGC
  >Rosalind_0808
  CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC
  TGGGAACCTGCGGGCAGTAGGTGGAAT";

assert_eq!(best_gc_content_in_dataset(dataset).unwrap(),
  GCcontent {string_id: "Rosalind_0808".to_string(), gc_content: 60.919540f32});

孟德尔的第一个定律

示例

use rosalind::RosalindError::InvalidInputParameters;
use rosalind::iprb::*;

assert_eq!(dominant_allele_probability(0, 1, 1).unwrap_err(), InvalidInputParameters);
assert_eq!(dominant_allele_probability(1, 0, 1).unwrap_err(), InvalidInputParameters);
assert_eq!(dominant_allele_probability(1, 1, 0).unwrap_err(), InvalidInputParameters);

assert_eq!(dominant_allele_probability(2, 2, 2).unwrap(), 0.7833333);

共识和轮廓

示例

use rosalind::cons::*;

let prof = Profile {
    A: vec![5, 1, 0, 0, 5, 5, 0, 0],
    C: vec![0, 0, 1, 4, 2, 0, 6, 1],
    G: vec![1, 1, 6, 3, 0, 1, 0, 0],
    T: vec![1, 5, 0, 0, 0, 1, 1, 6],
};

assert_eq!(consensus(prof).unwrap(), "ATGCAACT");

实用工具

将 Fasta 数据集解析为字符串列表

use rosalind::utils::*;

let fasta_dataset = ">Rosalind_1
    CCTGCGGAAG
    TCCCACTAAT
    >Rosalind_2
    CCATCGGTAG
    ATATCCATTT
    >Rosalind_3
    CCACCCTCGT
    TGGGAACCTG";

let expected_dataset = vec![
    "CCTGCGGAAGTCCCACTAAT",
    "CCATCGGTAGATATCCATTT",
    "CCACCCTCGTTGGGAACCTG",
];

assert_eq!(parse_fasta_dataset(fasta_dataset).unwrap(), expected_dataset);