60 lines
1.8 KiB
Perl
60 lines
1.8 KiB
Perl
package DDG::Goodie::ReverseComplement;
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# ABSTRACT: Give the DNA reverse complement of a DNA or RNA sequence.
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use strict;
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use DDG::Goodie;
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use feature 'state';
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triggers any => 'reverse complement', 'revcomp';
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zci answer_type => 'reverse_complement';
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zci is_cached => 1;
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name 'Reverse Complement';
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description 'Give the DNA reverse complement of a DNA or RNA sequence';
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primary_example_queries 'revcomp AAAACCCGGT';
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category 'transformations';
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topics 'science';
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code_url 'https://github.com/duckduckgo/zeroclickinfo-goodies/blob/master/lib/DDG/Goodie/ReverseComplement.pm';
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attribution github => ['http://github.com/wilkox', 'David Wilkins'];
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handle remainder => sub {
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my $sequence = $_;
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#Remove extra words if supplied
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$sequence =~ s/\bof\b//gi;
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$sequence =~ s/\bsequence\b//gi;
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$sequence =~ s/\b[DR]NA\b//gi;
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$sequence =~ s/\bnucleotide\b//gi;
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#Remove whitespace and dashes and make uppercase
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$sequence =~ s/\s|-//g;
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$sequence = uc($sequence);
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#Return nothing if sequence does not contains characters or contains characters
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# other than DNA/RNA bases or standard IUPAC ambiguity codes
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return unless ($sequence =~ /^[ATCGURYKMSWBVDHN]+$/);
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my $normalized_seq = $sequence;
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#DNA contains thymine (T) but not uracil (U);
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# RNA contains U but not T (with some extremely
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# rare exceptions). Hence, if the sequence
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# contains both U and T it's more likely to be an
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# error than a real molecule so should return nothing.
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return if $sequence =~ /T/ && $sequence =~ /U/;
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#Complement, using standard IUPAC codes
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$sequence =~ tr/ATUCGRYKMBVHD/TAAGCYRMKVBDH/;
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#Reverse
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$sequence = reverse($sequence);
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return $sequence,
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structured_answer => {
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input => [$normalized_seq],
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operation => 'Nucleotide reverse complement',
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result => $sequence
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};
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};
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1;
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