Transitions and Transversions

AUTHOR

L. Grondin

http://rosalind.info/problems/tran/

Sample input

>Rosalind_0209
    GCAACGCACAACGAAAACCCTTAGGGACTGGATTATTTCGTGATCGTTGTAGTTATTGGA
    AGTACGGGCATCAACCCAGTT
    >Rosalind_2200
    TTATCTGACAAAGAAAGCCGTCAACGGCTGGATAATTTCGCGATCGTGCTGGTTACTGGC
    GGTACGAGTGTTCCTTTGGGT

Sample output

1.21428571429
use v6;



my $default-input = q:to/END/;
    >Rosalind_0209
    GCAACGCACAACGAAAACCCTTAGGGACTGGATTATTTCGTGATCGTTGTAGTTATTGGA
    AGTACGGGCATCAACCCAGTT
    >Rosalind_2200
    TTATCTGACAAAGAAAGCCGTCAACGGCTGGATAATTTCGCGATCGTGCTGGTTACTGGC
    GGTACGAGTGTTCCTTTGGGT
    END

sub MAIN($input-file = Nil) {
    my $input = $input-file ?? $input-file.IO.slurp !! $default-input;
    given $input {
        my @dna;
        for m:g/ '>Rosalind_' <.digit>**4 \n ( <[ACGT\n]>+ ) / {
            push @dna, $_[0].subst: "\n", '', :g;
        }
        my ($transitions, $transversions);
        for (@dna[0].comb Z @dna[1].comb).flat -> $a, $b {
            next unless $a ne $b;
            if "$a$b" eq any <AG GA CT TC> { $transitions++ }
            else { $transversions++ }
        }
        say ($transitions/$transversions).fmt("%0.11f");
    }
}

# vim: expandtab shiftwidth=4 ft=perl6

See Also

afrq-grondilu.pl

Counting Disease Carriers

aspc-grondilu.pl

Introduction to Alternative Splicing

cons-grondilu.pl

Consensus and Profile

conv-grondilu.pl

Comparing Spectra with the Spectral Convolution

cstr-grondilu.pl

Creating a Character Table from Genetic Strings

ctbl-grondilu.pl

Creating a Character Table

dbpr-grondilu.pl

Introduction to Protein Databases

dna-gerdr.pl

Counting DNA Nucleotides

dna-grondilu.pl

Counting DNA Nucleotides

eubt-grondilu.pl

Enumerating Unrooted Binary Trees

eval-grondilu.pl

Expected Number of Restriction Sites

fib-grondilu.pl

Rabbits and Recurrence Relations

fibd-grondilu.pl

Mortal Fibonacci Rabbits

gc-gerdr.pl

Computing GC Content

grph-grondilu.pl

Overlap Graphs

hamm-grondilu.pl

Counting Point Mutations

iev-grondilu.pl

Calculating Expected Offspring

indc-grondilu.pl

Independent Segregation of Chromosomes

iprb-grondilu.pl

Mendel's First Law

itwv-grondilu.pl

Finding Disjoint Motifs in a Gene

lcsq-grondilu.pl

Finding a Shared Spliced Motif

lia-grondilu.pl

Independent Alleles

lrep-grondilu-p5.pl

mmch-grondilu.pl

Maximum Matchings and RNA Secondary Structures

mprt-grondilu.pl

Finding a Protein Motif

mrna-grondilu.pl

Inferring mRNA from Protein

nwck-grondilu.pl

Distances in Trees

orf-grondilu.pl

Open Reading Frames

pmch-grondilu.pl

Perfect Matchings and RNA Secondary Structures

pper-grondilu.pl

Partial Permutations

prob-grondilu.pl

Introduction to Random Strings

qrt-grondilu.pl

Quartets

README.md

revc-gerdr.pl

Complementing a Strand of DNA

rna-gerdr.pl

Transcribing DNA into RNA

rstr-grondilu.pl

Matching Random Motifs

sexl-grondilu.pl

Sex-Linked Inheritance

sgra-grondilu.pl

Using the Spectrum Graph to Infer Peptides

spec-grondilu.pl

Inferring Protein from Spectrum

sseq-grondilu.pl

Finding a Spliced Motif

subs-grondilu.pl

Finding a Motif in DNA

suff-grondilu.pl

Encoding Suffix Trees

trie-grondilu.pl

Introduction to Pattern Matching

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