Bioinformatics/Global alignment: Difference between revisions
Content added Content deleted
SqrtNegInf (talk | contribs) m (→{{header|Raku}}: more idiomatic) |
m (→{{header|Raku}}: Thanks SqrtNegInf for the Rakuish uplifts ; some obsessive but insignificant changes ; it seems a little bit slower with the default topic array variable ?) |
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sub printCounts(\seq) { |
sub printCounts(\seq) { |
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my |
my $bases = seq.comb.Bag ; |
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say "\nNucleotide counts for ", seq, " :"; |
say "\nNucleotide counts for ", seq, " :"; |
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say |
say $bases.kv, " and total length = ", $bases.total |
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} |
} |
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S1 = s1.substr: $offset ; |
S1 = s1.substr: $offset ; |
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with S1.index(s2.substr(0,1)) -> $p { $offset += $p } else { return False } |
with S1.index(s2.substr(0,1)) -> $p { $offset += $p } else { return False } |
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return s1.chars - $offset if s2.starts-with: s1.substr: $offset |
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return s1.chars - $offset if s2.starts-with: S1 |
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} |
} |
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} |
} |
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sub shortestCommonSuperstring { |
sub shortestCommonSuperstring { |
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my @ss = deduplicate @_ ; |
my \ß = $ = [~] my @ss = deduplicate @_ ; # ShortestSuper |
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my \ß = $ = [~] @ss ; # ShortestSuper |
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for @ss.permutations -> @perm { |
for @ss.permutations -> @perm { |
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my \sup = $ = @perm[0]; |
my \sup = $ = @perm[0]; |
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for @perm.rotor(2 => -1) |
for @perm.rotor(2 => -1) { sup ~= @_[1].substr: stringCentipede |@_ } |
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my \overlapPos = stringCentipede |@duo[0,1]; |
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sup ~= @duo[1].substr: overlapPos; |
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} |
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ß = sup if sup.chars < ß.chars ; |
ß = sup if sup.chars < ß.chars ; |
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} |
} |
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