zeroclickinfo-goodies/t/ReverseComplement.t

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Perl
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#!/usr/bin/env perl
use strict;
use warnings;
use Test::More;
use DDG::Test::Goodie;
zci answer_type => 'reverse_complement';
zci is_cached => 1;
my @aaaacccggt = (
"ACCGGGTTTT",
structured_answer => {
input => ['AAAACCCGGT'],
operation => 'Nucleotide reverse complement',
result => 'ACCGGGTTTT'
});
ddg_goodie_test(
[qw( DDG::Goodie::ReverseComplement)],
#Basic DNA reverse complements, various trigger combinations
'AAAACCCGGT reverse complement' => test_zci(@aaaacccggt),
'reverse complement of TTTGATCATGGCTCAGGACGAACGCTGGCGGCGT' => test_zci(
"ACGCCGCCAGCGTTCGTCCTGAGCCATGATCAAA",
structured_answer => {
input => ['TTTGATCATGGCTCAGGACGAACGCTGGCGGCGT'],
operation => 'Nucleotide reverse complement',
result => 'ACGCCGCCAGCGTTCGTCCTGAGCCATGATCAAA'
}
),
'AAAACCCGGT revcomp' => test_zci(@aaaacccggt),
'revcomp AAAACCCGGT' => test_zci(@aaaacccggt),
'revcomp of AAAACCCGGT' => test_zci(@aaaacccggt),
'DNA revcomp of sequence AAAACCCGGT' => test_zci(@aaaacccggt),
'reverse complement of RNA sequence AAAACCCGGU' => test_zci(
"ACCGGGTTTT",
structured_answer => {
input => ['AAAACCCGGU'],
operation => 'Nucleotide reverse complement',
result => 'ACCGGGTTTT'
}
),
#RNA reverse complement with acceptable spacing characters
'reverse complement uca gac gga' => test_zci(
"TCCGTCTGA",
structured_answer => {
input => ['UCAGACGGA'],
operation => 'Nucleotide reverse complement',
result => 'TCCGTCTGA',
}
),
'reverse complement of nucleotide sequence uca-gac-gga' => test_zci(
"TCCGTCTGA",
structured_answer => {
input => ['UCAGACGGA'],
operation => 'Nucleotide reverse complement',
result => 'TCCGTCTGA',
}
),
#With ambiguous bases (both DNA and RNA)
'reverse complement TCAAAWWDGGATTAMATACCCTGGTAGTCCACRCCATAAACGATGTATGCTTGGTGRGVGTGAGTAATCACTCAGTMCGAAGGCAACCTGATAAGCATACCKCCTVGAGTACGATCSCAAGGTTGAAACTCA DNA sequence'
=> test_zci(
"TGAGTTTCAACCTTGSGATCGTACTCBAGGMGGTATGCTTATCAGGTTGCCTTCGKACTGAGTGATTACTCACBCYCACCAAGCATACATCGTTTATGGYGTGGACTACCAGGGTATKTAATCCHWWTTTGA",
structured_answer => {
input => [
'TCAAAWWDGGATTAMATACCCTGGTAGTCCACRCCATAAACGATGTATGCTTGGTGRGVGTGAGTAATCACTCAGTMCGAAGGCAACCTGATAAGCATACCKCCTVGAGTACGATCSCAAGGTTGAAACTCA'
],
operation => 'Nucleotide reverse complement',
result =>
'TGAGTTTCAACCTTGSGATCGTACTCBAGGMGGTATGCTTATCAGGTTGCCTTCGKACTGAGTGATTACTCACBCYCACCAAGCATACATCGTTTATGGYGTGGACTACCAGGGTATKTAATCCHWWTTTGA'
},
),
'reverse complement CUAKCCAAGCCGACGASUCGGUAGCUGGUCUGAGAGKGACGAACAGCCACACUGGAACUGAGACAYCGGUCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGUCAAKUGGACRGCAAGUCUGAACCAYGCGACGRCGCGUGCGGGAUGAAGGGGCUUAGCCUCGUAAACDCGCURGUCAAGAGGGACGAGAGGHGCGAUUUUGUMCGUCCGGGWWACGV'
=> test_zci(
"BCGTWWCCCGGACGKACAAAATCGCDCCTCTCGTCCCTCTTGACYAGCGHGTTTACGAGGCTAAGCCCCTTCATCCCGCACGCGYCGTCGCRTGGTTCAGACTTGCYGTCCAMTTGACCAATATTCCTCACTGCTGCCTCCCGTAGGAGTCTGGACCGRTGTCTCAGTTCCAGTGTGGCTGTTCGTCMCTCTCAGACCAGCTACCGASTCGTCGGCTTGGMTAG",
structured_answer => {
input => [
'CUAKCCAAGCCGACGASUCGGUAGCUGGUCUGAGAGKGACGAACAGCCACACUGGAACUGAGACAYCGGUCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGUCAAKUGGACRGCAAGUCUGAACCAYGCGACGRCGCGUGCGGGAUGAAGGGGCUUAGCCUCGUAAACDCGCURGUCAAGAGGGACGAGAGGHGCGAUUUUGUMCGUCCGGGWWACGV'
],
operation => 'Nucleotide reverse complement',
result =>
'BCGTWWCCCGGACGKACAAAATCGCDCCTCTCGTCCCTCTTGACYAGCGHGTTTACGAGGCTAAGCCCCTTCATCCCGCACGCGYCGTCGCRTGGTTCAGACTTGCYGTCCAMTTGACCAATATTCCTCACTGCTGCCTCCCGTAGGAGTCTGGACCGRTGTCTCAGTTCCAGTGTGGCTGTTCGTCMCTCTCAGACCAGCTACCGASTCGTCGGCTTGGMTAG'
},
),
#Mix of DNA and RNA bases (should return empty, as it is more likely that this
# is an error than one of the edge cases of uracil-containing DNA)
'reverse complement AAATTTCCCGGGUUU' => undef,
#Non-nucleic acid query strings (should return empty, no idea what they wanted)
'reverse complement hello-this-is-DNA' => undef,
'DNA reverse complement' => undef,
);
done_testing;