Bioinformatics/Global alignment: Difference between revisions

</pre>

=={{header|Raku}}==

{{trans|Go}}

{{trans|Julia}}

<lang perl6># 20210209 Raku programming solution

sub printCounts(\seq) {

my %bases = seq.comb.Bag ;

say "\nNucleotide counts for ", seq, " :";

say %bases.kv, " and total length = ", %bases.values.sum

}

sub stringCentipede(\s1, \s2) {

loop ( my $offset = 0, my \S1 = $ = '' ; ; $offset++ ) {

S1 = s1.substr: $offset ;

with S1.index(s2.substr(0,1)) -> $p { $offset += $p } else { return 0 }

S1 = s1.substr: $offset ;

return s1.chars - $offset if s2.starts-with: S1

}

}

sub deduplicate {

my @sorted = @_.unique.sort: { $^a.chars <=> $^b.chars } ; # by length

gather while ( my $target = shift @sorted ) {

take $target unless @sorted.grep: { .contains: $target }

}

}

sub shortestCommonSuperstring {

my @ss = deduplicate @_ ;

my \ß = $ = [~] @ss ; # ShortestSuper

for @ss.permutations -> @perm {

my \sup = $ = @perm[0];

for @perm.rotor(2 => -1) -> @duo {

my \overlapPos = stringCentipede @duo[0], @duo[1];

sup ~= @duo[1].substr: overlapPos;

}

ß = sup if sup.chars < ß.chars ;

}

ß

}

.&shortestCommonSuperstring.&printCounts for (

<TA AAG TA GAA TA>,

<CATTAGGG ATTAG GGG TA>,

<AAGAUGGA GGAGCGCAUC AUCGCAAUAAGGA> ,

<ATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTAT

GGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGT

CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA

TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC

AACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT

GCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTC

CGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCT

TGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC

CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGC

GATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATT

TTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATC

CTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA

TCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGA

>,

)

</lang>

{{out}}

<pre>

Nucleotide counts for TAAGAA :

(T 1 A 4 G 1) and total length = 6

Nucleotide counts for CATTAGGG :

(G 3 A 2 T 2 C 1) and total length = 8

Nucleotide counts for AAGAUGGAGCGCAUCGCAAUAAGGA :

(A 10 U 3 C 4 G 8) and total length = 25

Nucleotide counts for CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA :

(C 57 G 75 A 74 T 94) and total length = 300