ReverseComplement: Switching to text template
Rob Emery
parent
e71eb3c5d4
commit
3c152febc2
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@ -12,39 +12,41 @@ zci is_cached => 1;
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handle remainder => sub {
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handle remainder => sub {
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my $sequence = $_;
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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/ && $sequence =~ /U/;
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#Remove extra words if supplied
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#Complement, using standard IUPAC codes
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$sequence =~ s/\bof\b//gi;
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$sequence =~ tr/ATUCGRYKMBVHD/TAAGCYRMKVBDH/;
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$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/ && $sequence =~ /U/;
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#Complement, using standard IUPAC codes
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#Reverse
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$sequence =~ tr/ATUCGRYKMBVHD/TAAGCYRMKVBDH/;
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$sequence = reverse($sequence);
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#Reverse
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return $sequence, structured_answer => {
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$sequence = reverse($sequence);
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data => {
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title => $sequence,
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return $sequence,
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subtitle => "Nucleotide reverse complement: $normalized_seq"
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structured_answer => {
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},
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input => [$normalized_seq],
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templates => {
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operation => 'Nucleotide reverse complement',
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group => 'text'
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result => $sequence
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}
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};
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};
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};
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};
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@ -9,82 +9,47 @@ use DDG::Test::Goodie;
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zci answer_type => 'reverse_complement';
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zci answer_type => 'reverse_complement';
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zci is_cached => 1;
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zci is_cached => 1;
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my @aaaacccggt = (
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my @aaaacccggt = ("ACCGGGTTTT",'AAAACCCGGT');
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"ACCGGGTTTT",
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structured_answer => {
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sub build_test {
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input => ['AAAACCCGGT'],
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my ($answer, $input) = @_;
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operation => 'Nucleotide reverse complement',
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return test_zci($answer, structured_answer => {
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result => 'ACCGGGTTTT'
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data => {
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});
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title => $answer,
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subtitle => "Nucleotide reverse complement: $input"
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},
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templates => {
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group => 'text'
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}
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})
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}
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ddg_goodie_test(
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ddg_goodie_test(
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[qw( DDG::Goodie::ReverseComplement)],
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[qw( DDG::Goodie::ReverseComplement)],
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#Basic DNA reverse complements, various trigger combinations
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#Basic DNA reverse complements, various trigger combinations
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'AAAACCCGGT reverse complement' => test_zci(@aaaacccggt),
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'AAAACCCGGT reverse complement' => build_test(@aaaacccggt),
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'reverse complement of TTTGATCATGGCTCAGGACGAACGCTGGCGGCGT' => test_zci(
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'reverse complement of TTTGATCATGGCTCAGGACGAACGCTGGCGGCGT' => build_test("ACGCCGCCAGCGTTCGTCCTGAGCCATGATCAAA", 'TTTGATCATGGCTCAGGACGAACGCTGGCGGCGT'),
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"ACGCCGCCAGCGTTCGTCCTGAGCCATGATCAAA",
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'AAAACCCGGT revcomp' => build_test(@aaaacccggt),
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structured_answer => {
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'revcomp AAAACCCGGT' => build_test(@aaaacccggt),
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input => ['TTTGATCATGGCTCAGGACGAACGCTGGCGGCGT'],
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'revcomp of AAAACCCGGT' => build_test(@aaaacccggt),
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operation => 'Nucleotide reverse complement',
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'DNA revcomp of sequence AAAACCCGGT' => build_test(@aaaacccggt),
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result => 'ACGCCGCCAGCGTTCGTCCTGAGCCATGATCAAA'
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'reverse complement of RNA sequence AAAACCCGGU' => build_test("ACCGGGTTTT", 'AAAACCCGGU'),
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}
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),
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'AAAACCCGGT revcomp' => test_zci(@aaaacccggt),
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'revcomp AAAACCCGGT' => test_zci(@aaaacccggt),
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'revcomp of AAAACCCGGT' => test_zci(@aaaacccggt),
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'DNA revcomp of sequence AAAACCCGGT' => test_zci(@aaaacccggt),
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'reverse complement of RNA sequence AAAACCCGGU' => test_zci(
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"ACCGGGTTTT",
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structured_answer => {
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input => ['AAAACCCGGU'],
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operation => 'Nucleotide reverse complement',
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result => 'ACCGGGTTTT'
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}
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),
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#RNA reverse complement with acceptable spacing characters
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#RNA reverse complement with acceptable spacing characters
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'reverse complement uca gac gga' => test_zci(
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'reverse complement uca gac gga' => build_test("TCCGTCTGA", 'UCAGACGGA'),
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"TCCGTCTGA",
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'reverse complement of nucleotide sequence uca-gac-gga' => build_test("TCCGTCTGA", 'UCAGACGGA'),
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structured_answer => {
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input => ['UCAGACGGA'],
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operation => 'Nucleotide reverse complement',
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result => 'TCCGTCTGA',
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}
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),
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'reverse complement of nucleotide sequence uca-gac-gga' => test_zci(
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"TCCGTCTGA",
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structured_answer => {
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input => ['UCAGACGGA'],
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operation => 'Nucleotide reverse complement',
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result => 'TCCGTCTGA',
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}
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),
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#With ambiguous bases (both DNA and RNA)
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#With ambiguous bases (both DNA and RNA)
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'reverse complement TCAAAWWDGGATTAMATACCCTGGTAGTCCACRCCATAAACGATGTATGCTTGGTGRGVGTGAGTAATCACTCAGTMCGAAGGCAACCTGATAAGCATACCKCCTVGAGTACGATCSCAAGGTTGAAACTCA DNA sequence'
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'reverse complement TCAAAWWDGGATTAMATACCCTGGTAGTCCACRCCATAAACGATGTATGCTTGGTGRGVGTGAGTAATCACTCAGTMCGAAGGCAACCTGATAAGCATACCKCCTVGAGTACGATCSCAAGGTTGAAACTCA DNA sequence'
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=> test_zci(
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=> build_test(
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"TGAGTTTCAACCTTGSGATCGTACTCBAGGMGGTATGCTTATCAGGTTGCCTTCGKACTGAGTGATTACTCACBCYCACCAAGCATACATCGTTTATGGYGTGGACTACCAGGGTATKTAATCCHWWTTTGA",
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"TGAGTTTCAACCTTGSGATCGTACTCBAGGMGGTATGCTTATCAGGTTGCCTTCGKACTGAGTGATTACTCACBCYCACCAAGCATACATCGTTTATGGYGTGGACTACCAGGGTATKTAATCCHWWTTTGA",
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structured_answer => {
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'TCAAAWWDGGATTAMATACCCTGGTAGTCCACRCCATAAACGATGTATGCTTGGTGRGVGTGAGTAATCACTCAGTMCGAAGGCAACCTGATAAGCATACCKCCTVGAGTACGATCSCAAGGTTGAAACTCA'
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input => [
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),
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'TCAAAWWDGGATTAMATACCCTGGTAGTCCACRCCATAAACGATGTATGCTTGGTGRGVGTGAGTAATCACTCAGTMCGAAGGCAACCTGATAAGCATACCKCCTVGAGTACGATCSCAAGGTTGAAACTCA'
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],
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operation => 'Nucleotide reverse complement',
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result =>
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'TGAGTTTCAACCTTGSGATCGTACTCBAGGMGGTATGCTTATCAGGTTGCCTTCGKACTGAGTGATTACTCACBCYCACCAAGCATACATCGTTTATGGYGTGGACTACCAGGGTATKTAATCCHWWTTTGA'
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},
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),
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'reverse complement CUAKCCAAGCCGACGASUCGGUAGCUGGUCUGAGAGKGACGAACAGCCACACUGGAACUGAGACAYCGGUCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGUCAAKUGGACRGCAAGUCUGAACCAYGCGACGRCGCGUGCGGGAUGAAGGGGCUUAGCCUCGUAAACDCGCURGUCAAGAGGGACGAGAGGHGCGAUUUUGUMCGUCCGGGWWACGV'
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'reverse complement CUAKCCAAGCCGACGASUCGGUAGCUGGUCUGAGAGKGACGAACAGCCACACUGGAACUGAGACAYCGGUCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGUCAAKUGGACRGCAAGUCUGAACCAYGCGACGRCGCGUGCGGGAUGAAGGGGCUUAGCCUCGUAAACDCGCURGUCAAGAGGGACGAGAGGHGCGAUUUUGUMCGUCCGGGWWACGV'
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=> test_zci(
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=> build_test(
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"BCGTWWCCCGGACGKACAAAATCGCDCCTCTCGTCCCTCTTGACYAGCGHGTTTACGAGGCTAAGCCCCTTCATCCCGCACGCGYCGTCGCRTGGTTCAGACTTGCYGTCCAMTTGACCAATATTCCTCACTGCTGCCTCCCGTAGGAGTCTGGACCGRTGTCTCAGTTCCAGTGTGGCTGTTCGTCMCTCTCAGACCAGCTACCGASTCGTCGGCTTGGMTAG",
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"BCGTWWCCCGGACGKACAAAATCGCDCCTCTCGTCCCTCTTGACYAGCGHGTTTACGAGGCTAAGCCCCTTCATCCCGCACGCGYCGTCGCRTGGTTCAGACTTGCYGTCCAMTTGACCAATATTCCTCACTGCTGCCTCCCGTAGGAGTCTGGACCGRTGTCTCAGTTCCAGTGTGGCTGTTCGTCMCTCTCAGACCAGCTACCGASTCGTCGGCTTGGMTAG",
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structured_answer => {
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'CUAKCCAAGCCGACGASUCGGUAGCUGGUCUGAGAGKGACGAACAGCCACACUGGAACUGAGACAYCGGUCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGUCAAKUGGACRGCAAGUCUGAACCAYGCGACGRCGCGUGCGGGAUGAAGGGGCUUAGCCUCGUAAACDCGCURGUCAAGAGGGACGAGAGGHGCGAUUUUGUMCGUCCGGGWWACGV',
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input => [
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'CUAKCCAAGCCGACGASUCGGUAGCUGGUCUGAGAGKGACGAACAGCCACACUGGAACUGAGACAYCGGUCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGUCAAKUGGACRGCAAGUCUGAACCAYGCGACGRCGCGUGCGGGAUGAAGGGGCUUAGCCUCGUAAACDCGCURGUCAAGAGGGACGAGAGGHGCGAUUUUGUMCGUCCGGGWWACGV'
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],
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operation => 'Nucleotide reverse complement',
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result =>
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'BCGTWWCCCGGACGKACAAAATCGCDCCTCTCGTCCCTCTTGACYAGCGHGTTTACGAGGCTAAGCCCCTTCATCCCGCACGCGYCGTCGCRTGGTTCAGACTTGCYGTCCAMTTGACCAATATTCCTCACTGCTGCCTCCCGTAGGAGTCTGGACCGRTGTCTCAGTTCCAGTGTGGCTGTTCGTCMCTCTCAGACCAGCTACCGASTCGTCGGCTTGGMTAG'
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},
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),
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),
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#Mix of DNA and RNA bases (should return empty, as it is more likely that this
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#Mix of DNA and RNA bases (should return empty, as it is more likely that this
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