void testRevcompRepresentative() {
list<Sequence> reads = Fasta("../../data/representative_revcomp.fa").getAll();
KmerRepresentativeComputer krc(reads, "##############");
krc.setOptions(false, 3, 0.5);
krc.setCoverageReferenceLength(50);
krc.compute();
Sequence representative = krc.getRepresentative();
// Computing reads revcomp
for (list <Sequence>::iterator it = reads.begin(); it != reads.end(); it++) {
it->sequence = revcomp(it->sequence);
}
KmerRepresentativeComputer krc2(reads, "##############");
krc2.setOptions(false, 3, 0.5);
krc2.setCoverageReferenceLength(50);
krc2.compute();
Sequence representative2 = krc2.getRepresentative();
// Check position of [ in label, so that we remove that part, and then we
// can compare the labels
size_t pos1 = representative.label.find_first_of('[');
size_t pos2 = representative2.label.find_first_of('[');
TAP_TEST(representative.label.substr(0, pos1) == representative2.label.substr(0, pos2), TEST_KMER_REPRESENTATIVE_REVCOMP,
"The two representatives should have the same label");
TAP_TEST(revcomp(representative.sequence) == representative2.sequence, TEST_KMER_REPRESENTATIVE_REVCOMP,
"The two representatives should have the same sequence (but revcomp-ed)");
}
void testFastaNbSequences() {
TAP_TEST(nb_sequences_in_fasta("../../germline/IGHV.fa") == 348, TEST_FASTA_NB_SEQUENCES, "ccc");
int a1 = approx_nb_sequences_in_fasta("../../germline/IGHV.fa");
TAP_TEST(a1 >= 340 && a1 <= 348, TEST_FASTA_NB_SEQUENCES, "");
int a2 = nb_sequences_in_fasta("../../data/Stanford_S22.fasta", true);
TAP_TEST(a2 >= 13100 && a2 <= 13200, TEST_FASTA_NB_SEQUENCES, "");
}
void testSequenceOutputOperator() {
ostringstream oss;
Sequence seq = {"a b c", "a", "GATTACA", "AIIIIIH", NULL};
oss << seq;
TAP_TEST(oss.str() == "@a\nGATTACA\n+\nAIIIIIH\n", TEST_SEQUENCE_OUT, oss.str());
ostringstream oss2;
seq.quality = "";
oss2 << seq;
TAP_TEST(oss2.str() == ">a\nGATTACA\n", TEST_SEQUENCE_OUT, oss.str());
}
void testFastaAdd() {
Fasta fa1("../../data/test1.fa");
Fasta fa2("../../data/test1.fa");
fa2.add("../../data/test1.fa");
TAP_TEST(fa1.size() * 2 == fa2.size(), TEST_FASTA_ADD, "");
for (int i=0; i < fa1.size(); i++) {
TAP_TEST(fa1.label(i) == fa2.label(i)
&& fa1.label(i) == fa2.label(i+fa1.size()), TEST_FASTA_ADD, "");
TAP_TEST(fa1.label_full(i) == fa2.label_full(i)
&& fa1.label_full(i) == fa2.label_full(i+fa1.size()),
TEST_FASTA_ADD, "");
TAP_TEST(fa1.sequence(i) == fa2.sequence(i)
&& fa1.sequence(i) == fa2.sequence(i+fa1.size()),
TEST_FASTA_ADD, "");
}
}
void testScore() {
// ReadLengthScore testing
ReadLengthScore rls;
Sequence seq1 = {"seq", "seq", "", "", 0};
TAP_TEST_EQUAL(rls.getScore(seq1), 0., TEST_LENGTH_SCORE,
"score should be 0, is " << rls.getScore(seq1));
Sequence seq2 = {"seq", "seq", "ATCGTTTACGTC", "", 0};
TAP_TEST_EQUAL(rls.getScore(seq2), 12., TEST_LENGTH_SCORE,
"score should be 12, is " << rls.getScore(seq2));
Sequence seq3 = {"seq", "seq", "A", "", 0};
TAP_TEST_EQUAL(rls.getScore(seq3), 1., TEST_LENGTH_SCORE,
"score should be 1, is " << rls.getScore(seq3));
// ReadQualityScore testing
ReadQualityScore rqs;
Sequence seq4 = {"s", "s", "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII", 0};
TAP_TEST((int) rqs.getScore(seq4) == (int) (41 * 120/ GOOD_QUALITY), TEST_QUALITY_SCORE,
"score should be " << (int) (41 * 120/ GOOD_QUALITY) << " not " << rqs.getScore(seq4));
// Changing the quality, put the percentile should not change yet.
seq4.quality[10] = '-';
TAP_TEST((int) rqs.getScore(seq4) == (int) (41 * 120/ GOOD_QUALITY), TEST_QUALITY_SCORE,
"score should be " << (int) (41 * 120/ GOOD_QUALITY) << " not " << rqs.getScore(seq4));
// Now the percentile value should change and should correspond to '-'
seq4.quality[22] = '!';
TAP_TEST((int) rqs.getScore(seq4) == (int) (('-' - ' ') * 120/ GOOD_QUALITY), TEST_QUALITY_SCORE,
"score should be " << (int) (('-' - ' ') * 120/ GOOD_QUALITY) << " not " << rqs.getScore(seq4));
// Quality does not exist anymore → the score is the length
seq4.quality = "";
TAP_TEST_EQUAL(rqs.getScore(seq4), 120, TEST_QUALITY_SCORE,
"score should be 120 not " << rqs.getScore(seq4));
}
void testExtendedNucleotides() {
TAP_TEST(is_extended_nucleotide('A') == false, TEST_EXTENDED_NUCL, "");
TAP_TEST(is_extended_nucleotide('a') == false, TEST_EXTENDED_NUCL, "");
TAP_TEST(is_extended_nucleotide('N') == true, TEST_EXTENDED_NUCL, "");
TAP_TEST(is_extended_nucleotide(' ') == true, TEST_EXTENDED_NUCL, "");
TAP_TEST(has_extended_nucleotides("") == false, TEST_EXTENDED_NUCL, "");
TAP_TEST(has_extended_nucleotides("ACGTacgt") == false, TEST_EXTENDED_NUCL, "");
TAP_TEST(has_extended_nucleotides("ACGTnacgt") == true, TEST_EXTENDED_NUCL, "");
}
void testChooser() {
list<Sequence> reads = BioReader("data/test1.fa").getAll();
ReadLengthScore rls;
ReadChooser rc(reads, rls);
TAP_TEST(rc.getithBest(1).label == "seq4", TEST_READ_CHOOSER_SORTED,
"First sequence is " << rc.getithBest(1).label);
TAP_TEST(rc.getithBest(1).label == rc.getBest().label
&& rc.getithBest(1).sequence == rc.getBest().sequence,
TEST_READ_CHOOSER_BEST,"");
TAP_TEST(rc.getithBest(2).label == "seq2", TEST_READ_CHOOSER_SORTED,
"Second sequence is " << rc.getithBest(2).label);
TAP_TEST(rc.getithBest(3).label == "seq1", TEST_READ_CHOOSER_SORTED,
"Third sequence is " << rc.getithBest(3).label);
TAP_TEST(rc.getithBest(4).label == "", TEST_READ_CHOOSER_SORTED,
"First sequence is " << rc.getithBest(4).label);
}
void testFasta1() {
Fasta fa("../../data/test1.fa");
Fasta fq("../../data/test1.fq");
TAP_TEST(fa.size() == fq.size(), TEST_FASTA_SIZE, "");
for (int i=0; i < fa.size(); i++) {
TAP_TEST(fa.label(i) == fq.label(i), TEST_FASTA_LABEL, "");
TAP_TEST(fa.label_full(i) == fq.label_full(i), TEST_FASTA_LABEL_FULL, "");
TAP_TEST(fa.sequence(i) == fq.sequence(i), TEST_FASTA_SEQUENCE, "");
}
TAP_TEST(fa.label(2) == "seq3", TEST_FASTA_LABEL, "");
TAP_TEST(fa.sequence(2) == "A", TEST_FASTA_SEQUENCE, "");
TAP_TEST(fa.label(4) == "", TEST_FASTA_LABEL, "");
TAP_TEST(fa.sequence(4) == "AATN", TEST_FASTA_SEQUENCE, "");
}
void testCreateSequence() {
Sequence seq1 = create_sequence("label", "l", "AAAAAAAAAA", "!!!!!!!!!!");
Sequence seq2 = create_sequence("", "", "", "");
TAP_TEST(seq1.label_full == "label", TEST_CREATE_SEQUENCE_LABEL_FULL, "");
TAP_TEST(seq2.label_full == "", TEST_CREATE_SEQUENCE_LABEL_FULL, "");
TAP_TEST(seq1.label == "l", TEST_CREATE_SEQUENCE_LABEL, "");
TAP_TEST(seq2.label == "", TEST_CREATE_SEQUENCE_LABEL, "");
TAP_TEST(seq1.sequence == "AAAAAAAAAA", TEST_CREATE_SEQUENCE_SEQUENCE, "");
TAP_TEST(seq2.sequence == "", TEST_CREATE_SEQUENCE_SEQUENCE, "");
TAP_TEST(seq1.quality == "!!!!!!!!!!", TEST_CREATE_SEQUENCE_QUALITY, "");
TAP_TEST(seq2.quality == "", TEST_CREATE_SEQUENCE_QUALITY, "");
}
void testRCInsertAcAutomaton() {
PointerACAutomaton<KmerAffect> aho(true);
aho.insert("ACAGTC", "V", true, 0, "##-##");
aho.build_failure_functions();
// Will insert AC-GT → ACAGT, ACCGT, ACGGT, ACTGT
// and CA-TC → CAATC, CACTC, CAGTC, CATTC
// plus the revcomps:
// Will insert GA-TG → GAATG, GACTG, GAGTG, GATTG
// and AC-GT → ACAGT, ACCGT, ACGGT, ACTGT
pointer_state<KmerAffect> *state = aho.goto_state("ACCGT");
TAP_TEST_EQUAL(state->informations.size(), 1, TEST_AC_GET, "");
TAP_TEST_EQUAL(state->informations.front(), AFFECT_AMBIGUOUS, TEST_AC_GET, "");
TAP_TEST(state->is_final, TEST_AC_FINAL, "");
TAP_TEST(! aho.goto_state("CAAT")->is_final, TEST_AC_FINAL, "");
TAP_TEST(aho.goto_state("CAAT")->informations.size() == 1, TEST_AC_GET, "");
TAP_TEST(aho.goto_state("CAAT")->informations.front() == AFFECT_UNKNOWN, TEST_AC_GET, "");
TAP_TEST(aho.goto_state("GAGTG")->informations.front() == AFFECT_V_BWD, TEST_AC_GET, "");
TAP_TEST(aho.goto_state("GAGTG")->is_final, TEST_AC_FINAL, "");
TAP_TEST(aho.goto_state("GAGTG")->transitions[A] == aho.goto_state("GA"), TEST_AC_TRANSITIONS, "");
vector<KmerAffect> results = aho.getResults("ACCGTgaatgCATTCA");
vector<KmerAffect> expected = {AFFECT_AMBIGUOUS,
AFFECT_UNKNOWN, AFFECT_UNKNOWN, AFFECT_UNKNOWN,
AFFECT_UNKNOWN, AFFECT_V_BWD, AFFECT_UNKNOWN,
AFFECT_UNKNOWN, AFFECT_UNKNOWN, AFFECT_UNKNOWN,
AFFECT_V, AFFECT_UNKNOWN, AFFECT_UNKNOWN, AFFECT_UNKNOWN, AFFECT_UNKNOWN,
AFFECT_UNKNOWN };
TAP_TEST(results.size() == expected.size(), TEST_AC_GET_RESULTS, "");
TAP_TEST(results == expected, TEST_AC_GET_RESULTS, "");
}
void testExtractBasename() {
TAP_TEST(extract_basename("/var/toto/titi/tutu/bla.bli.bluc", true) == "bla.bli",
TEST_EXTRACT_BASENAME, extract_basename("/var/toto/titi/tutu/bla.bli.bluc", true));
TAP_TEST(extract_basename("/var/toto/titi/tutu/bla.bli.bluc", false) == "bla.bli.bluc",
TEST_EXTRACT_BASENAME, extract_basename("/var/toto/titi/tutu/bla.bli.bluc", false));
TAP_TEST(extract_basename("bla.bli.bluc", true) == "bla.bli",
TEST_EXTRACT_BASENAME, extract_basename("bla.bli.bluc", true));
TAP_TEST(extract_basename("bla.bli.bluc", false) == "bla.bli.bluc",
TEST_EXTRACT_BASENAME, extract_basename("bla.bli.bluc", false));
TAP_TEST(extract_basename("a_filename_without_extension", true) == "a_filename_without_extension",
TEST_EXTRACT_BASENAME, extract_basename("a_filename_without_extension", true));
TAP_TEST(extract_basename("/", true) == "",
TEST_EXTRACT_BASENAME, extract_basename("/", true));
}
void testRepresentative() {
list<Sequence> reads = Fasta("../../data/representative.fa").getAll();
KmerRepresentativeComputer krc(reads, "##############");
krc.setStabilityLimit(0);
krc.setRevcomp(false);
krc.setMinCover(1);
krc.setPercentCoverage(0.5);
krc.setCoverageReferenceLength(50);
krc.compute();
Sequence representative = krc.getRepresentative();
// Seq3 is the longest it should be taken when performing 0 extra iteration
TAP_TEST(representative.label.find("seq3-[37,73]") == 0, TEST_KMER_REPRESENTATIVE,
"If we take the first representative we should have seq3, and not at the beginning (" << representative.label << " instead)");
krc.setStabilityLimit(1);
krc.compute();
representative = krc.getRepresentative();
TAP_TEST(representative.label.find("seq3-[37,73]") == 0, TEST_KMER_REPRESENTATIVE,
"When allowing one step before stability, we should still have seq3 (" << representative.label << " instead)");
krc.setStabilityLimit(2);
krc.compute();
representative = krc.getRepresentative();
TAP_TEST(representative.label.find("seq1-[0,41]") == 0, TEST_KMER_REPRESENTATIVE,
"When allowing two steps before stability, we should reach seq1 (" << representative.label << " instead)");
krc.setRevcomp(true);
krc.setRequiredSequence("ATCGCGCCCT"); // revcomp
krc.compute();
representative = krc.getRepresentative();
TAP_TEST(representative.label.find("seq2-[33,52]") == 0, TEST_KMER_REPRESENTATIVE_REQUIRED_SEQ,
"When requiring sequence ATCGCGCCCT, we should have seq2 (" << representative.label << " instead)");
krc.setRevcomp(false);
krc.compute();
TAP_TEST(! krc.hasRepresentative(), TEST_KMER_REPRESENTATIVE_REQUIRED_SEQ,
"When requiring sequence AGGGCGCGAT and revcomp=false, we shouldn't find anything (the sequence is revcomp-ed)");
krc.setRequiredSequence("");
krc.setMinCover(4);
krc.compute();
TAP_TEST(! krc.hasRepresentative(), TEST_KMER_REPRESENTATIVE,
"When requiring 4 reads to support the representative, we should not find any solution.");
}
void testLongest() {
list<Sequence> seqs;
seqs.push_back(create_sequence("seq1", "seq1", "AAAAAAAAA", ""));
seqs.push_back(create_sequence("seq2", "seq2", "AAAAA", ""));
seqs.push_back(create_sequence("seq3", "seq3", "AAAAAAAA", ""));
seqs.push_back(create_sequence("seq4", "seq4", "AAAAAAAAAA", ""));
seqs.push_back(create_sequence("seq5", "seq5", "AAAAAA", ""));
seqs.push_back(create_sequence("seq6", "seq6", "AAAAAAA", ""));
SequenceSampler s(seqs);
list<Sequence> l1 = s.getLongest(6, 11);
size_t *distrib = s.getLengthDistribution();
TAP_TEST(distrib[0] == 0
&& distrib[1] == 0 && distrib[2] == 0 && distrib[3] == 0 && distrib[4] == 0
&& distrib[5] == 1 && distrib[6] == 1 && distrib[7] == 1 && distrib[8] == 1
&& distrib[9] == 1 && distrib[10] == 1,
TEST_SAMPLER_LENGTH, "");
char id = '1';
TAP_TEST(l1.size() == 6, TEST_SAMPLER_LONGEST, "");
for (list<Sequence>::const_iterator it = l1.begin(); it != l1.end(); it++) {
TAP_TEST(it->label[3] == id, TEST_SAMPLER_LONGEST, "");
id++;
}
// With only 10 buckets, the two longest sequences share the same bucket.
// Due to their insertion order, the shorter will be sampled first
l1 = s.getLongest(2, 10);
distrib = s.getLengthDistribution();
TAP_TEST(distrib[0] == 0
&& distrib[1] == 0 && distrib[2] == 0 && distrib[3] == 0 && distrib[4] == 0
&& distrib[5] == 1 && distrib[6] == 1 && distrib[7] == 1 && distrib[8] == 1
&& distrib[9] == 2, TEST_SAMPLER_LENGTH, "");
TAP_TEST(l1.size() == 2, TEST_SAMPLER_LONGEST, "");
TAP_TEST(l1.front().sequence.size() == 9, TEST_SAMPLER_LONGEST, "");
Sequence next = *(++l1.begin());
TAP_TEST(next.sequence.size() == 10, TEST_SAMPLER_LONGEST, "label = " << next.label);
}
// Generate 10 sequences, and launch 10 times getRandom(1).
// We should not have the same sequence 10 times (p < 10^{-10})
void testRandom() {
list<Sequence> seqs;
string seg_name = "seq";
char id = '0';
string sequence = "AA";
for (int i = 0; i < 10; i++) {
seqs.push_back(create_sequence("seq" + string_of_int(id), "seq" + string_of_int(id), sequence, ""));
sequence += "A";
id++;
}
SequenceSampler sampler(seqs);
string first_random = sampler.getRandom(1).front().label;
bool all_equal = true;
for (int i = 0; i < 9 && all_equal; i++) {
if (first_random != sampler.getRandom(1).front().label)
all_equal = false;
}
TAP_TEST(all_equal == false, TEST_SAMPLER_RANDOM, "On the 10 trials, we drawn 10 times the same sequence");
}
void testOnlineFasta1() {
OnlineFasta fa("../../data/test1.fa");
OnlineFasta fq("../../data/test1.fq");
int nb_seq = 0;
TAP_TEST(fa.getLineNb() == 1, TEST_O_FASTA_LINE_NB, "");
TAP_TEST(fq.getLineNb() == 1, TEST_O_FASTA_LINE_NB, "");
while (fa.hasNext()) {
TAP_TEST(fq.hasNext(), TEST_O_FASTA_HAS_NEXT, "");
fa.next();
fq.next();
Sequence s1 = fa.getSequence();
Sequence s2 = fq.getSequence();
TAP_TEST(s1.label == s2.label && s1.label_full == s2.label_full
&& s1.sequence == s2.sequence, TEST_O_FASTA_GET_SEQUENCE, "fa: " << fa.getSequence() << endl << "fq: " << fq.getSequence());
nb_seq++;
}
TAP_TEST(fq.getLineNb() == 20, TEST_O_FASTA_LINE_NB, "");
TAP_TEST(! fq.hasNext(), TEST_O_FASTA_HAS_NEXT, "");
TAP_TEST(nb_seq == 5, TEST_O_FASTA_HAS_NEXT, "");
}
void testFastaAddThrows() {
bool caught = false;
try {
Fasta fa1("mlkdkklflskjfskldfj.fa");
} catch (invalid_argument e) {
TAP_TEST(string(e.what()).find("Error in opening file") != string::npos, TEST_FASTA_INVALID_FILE, "");
caught = true;
}
TAP_TEST(caught == true, TEST_FASTA_INVALID_FILE, "");
Fasta fa1("../../data/test1.fa");
caught = false;
try {
fa1.add("ljk:lkjsdfsdlfjsdlfkjs.fa");
} catch (invalid_argument e) {
TAP_TEST(string(e.what()).find("Error in opening file") != string::npos, TEST_FASTA_INVALID_FILE, "");
caught = true;
}
TAP_TEST(caught == true, TEST_FASTA_INVALID_FILE, "");
caught = false;
try {
fa1.add("testTools.cpp");
} catch (invalid_argument e) {
TAP_TEST(string(e.what()).find("The file seems to be malformed") != string::npos, TEST_FASTA_INVALID_FILE, "");
caught = true;
}
TAP_TEST(caught == true, TEST_FASTA_INVALID_FILE, "");
caught = false;
try {
OnlineFasta fa("lkjdflkdfjglkdfjg.fa");
} catch (invalid_argument e) {
TAP_TEST(string(e.what()).find("Error in opening file") != string::npos, TEST_FASTA_INVALID_FILE, "");
caught = true;
}
TAP_TEST(caught == true, TEST_FASTA_INVALID_FILE, "");
caught = false;
try {
Fasta fa1("../../data/malformed1.fq");
} catch (invalid_argument e) {
TAP_TEST(string(e.what()).find("Expected line starting with +") != string::npos, TEST_FASTA_INVALID_FILE, "");
caught = true;
}
TAP_TEST(caught == true, TEST_FASTA_INVALID_FILE, "");
caught = false;
try {
Fasta fa1("../../data/malformed2.fq");
} catch (invalid_argument e) {
TAP_TEST(string(e.what()).find("Unexpected EOF") == 0, TEST_FASTA_INVALID_FILE, "");
caught = true;
}
TAP_TEST(caught == true, TEST_FASTA_INVALID_FILE, "");
caught = false;
try {
Fasta fa1("../../data/malformed3.fq");
} catch (invalid_argument e) {
TAP_TEST(string(e.what()).find("Quality and sequence don't have the same length") == 0, TEST_FASTA_INVALID_FILE, "");
caught = true;
}
TAP_TEST(caught == true, TEST_FASTA_INVALID_FILE, "");
caught = false;
try {
Fasta fa1("../../data/malformed4.fq");
} catch (invalid_argument e) {
TAP_TEST(string(e.what()).find("Unexpected EOF") == 0, TEST_FASTA_INVALID_FILE, "");
caught = true;
}
TAP_TEST(caught == true, TEST_FASTA_INVALID_FILE, "");
caught = false;
try {
Fasta fa1("../../data/malformed5.fq");
} catch (invalid_argument e) {
TAP_TEST(string(e.what()).find("Unexpected EOF") == 0, TEST_FASTA_INVALID_FILE, "");
caught = true;
}
TAP_TEST(caught == true, TEST_FASTA_INVALID_FILE, "");
caught = false;
try {
// Can't test empty file with Fasta since we
// don't complain for empty files explicitly in Fasta constructor.
OnlineFasta fa1("../../data/malformed6.fq");
fa1.next();
} catch (invalid_argument e) {
TAP_TEST(string(e.what()).find("Unexpected EOF") == 0, TEST_FASTA_INVALID_FILE, "");
caught = true;
}
TAP_TEST(caught == true, TEST_FASTA_INVALID_FILE, "");
caught = false;
try {
Fasta fa1("../../data/malformed7.fq");
} catch(invalid_argument e) {
TAP_TEST(string(e.what()).find("Unexpected EOF") == 0, TEST_FASTA_INVALID_FILE, "");
caught = true;
}
TAP_TEST(caught == true, TEST_FASTA_INVALID_FILE, "");
}
void testNChooseK() {
TAP_TEST(nChoosek(1, 10) == 0, TEST_N_CHOOSE_K, "");
TAP_TEST(nChoosek(1, 1) == 1, TEST_N_CHOOSE_K, "");
TAP_TEST(nChoosek(5, 2) == 10, TEST_N_CHOOSE_K, "");
TAP_TEST(nChoosek(8, 4) == 70, TEST_N_CHOOSE_K, "");
}
/*
This test check the integrity of the getMultiResults function in
AbstractACAutomaton class and its inherited classes.
*/
void testGetMultiResults(){
map<KmerAffect,int> results;
PointerACAutomaton<KmerAffect> aho(false);
const string errorOccurence = "KmerAffect doesn't have the good number of occurences.";
const string errorSize = "Map has too many Kmers.";
seqtype seq = "TTTTAATTAAGGGGCTACCCCCAATGTCCGTGGAGCTCTGGGGGGTTA";
affect_t affect[10];
seqtype seqs[10];
char c = 'a';
for(int i = 0; i < 10; ++i){
affect[i].c = c;
c++;
}
seqs[0] = "AGCTCT";
seqs[1] = "TTTT";
seqs[2] = "AATT";
seqs[3] = "CGTGG";
seqs[4] = "CAATGTC";
seqs[5] = "AGGG";
seqs[6] = "GGGG";
seqs[7] = "TTAA";
seqs[8] = "GCTAC";
seqs[9] = "CCCC";
for(int i = 0;i < 10; ++i){
aho.insert(seqs[i], KmerAffect(affect[i]));
}
aho.build_failure_functions();
results = aho.getMultiResults(seq);
/* Best situation: every sequences is found at least once in automaton. */
TAP_TEST(results.size() <= 11, TEST_AC_OCCURENCES, errorSize);
TAP_TEST_EQUAL(results.at(aho.get(seqs[0])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[1])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[2])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[3])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[4])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[5])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[6])), 4, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[7])), 2, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[8])), 1, TEST_AC_OCCURENCES, errorOccurence);
TAP_TEST_EQUAL(results.at(aho.get(seqs[9])), 2, TEST_AC_OCCURENCES, errorOccurence);
/* Situation: Only one K-mer is in the sequence, appearing once. */
seqtype seq2 = "AAAAAAAAAAAAAAAAAATTCAAAAAAAAA";
results = aho.getMultiResults(seq2);
TAP_TEST(results.size() <= 2, TEST_AC_OCCURENCES, errorSize);
TAP_TEST_EQUAL(results.at(aho.get(seqs[2])), 1, TEST_AC_OCCURENCES, errorOccurence);
/* Situation: Only one K-mer is the sequence, appearing many times. */
seqtype seq3 = "GCTACGCTACGCTACGCTACGCTA";
results = aho.getMultiResults(seq3);
TAP_TEST(results.size() <= 2, TEST_AC_OCCURENCES, errorSize);
TAP_TEST_EQUAL(results.at(aho.get(seqs[8])), 4, TEST_AC_OCCURENCES, errorOccurence);
/* Situation: No K-mer appear in the sequence. */
seqtype seq4 = "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA";
results = aho.getMultiResults(seq4);
TAP_TEST(results.size() <= 1, TEST_AC_OCCURENCES, errorSize);
/*
If there is K-mers in automaton doesn't match the sequence, the map must
return only unknown K-mers.
*/
pair<KmerAffect, int> singleResult = *(results.begin());
KmerAffect unknownKmerAffect = singleResult.first;
TAP_TEST_EQUAL(unknownKmerAffect, AFFECT_UNKNOWN, TEST_AC_OCCURENCES, "Unknown Kmer not found");
}
void testSimpleInsertACAutomaton() {
PointerACAutomaton<Kmer> aho;
Kmer count_acag = Kmer("ACAG");
count_acag.count = 5;
Kmer count_caga = Kmer("CAGA");
count_caga.count = 2;
Kmer count_caca = Kmer("CACA");
count_caca.count = 3;
Kmer count_gca = Kmer("GCA");
count_gca.count = 1;
aho.insert("ACAG", count_acag);
aho.insert("CAGA", count_caga);
aho.insert("CACA", count_caca);
aho.insert("GCA", count_gca);
aho.build_failure_functions();
pointer_state<Kmer> *state_ac = aho.goto_state("ac");
pointer_state<Kmer> *state_aca = aho.goto_state("aca");
pointer_state<Kmer> *state_c = aho.goto_state("c");
pointer_state<Kmer> *state_g = aho.goto_state("g");
pointer_state<Kmer> *state_cag = aho.goto_state("cag");
TAP_TEST(aho.getInitialState()->transitions[T] == aho.getInitialState()
&& aho.getInitialState()->transitions[N] == aho.getInitialState(),
TEST_AC_TRANSITIONS, "");
TAP_TEST(state_ac->transitions[A] == state_aca, TEST_AC_TRANSITIONS, "");
TAP_TEST(state_ac->transitions[C] == state_c, TEST_AC_TRANSITIONS, "");
TAP_TEST(state_aca->transitions[A] == state_g->transitions[A], TEST_AC_TRANSITIONS, "");
TAP_TEST(state_c->transitions[C] == state_c, TEST_AC_TRANSITIONS, "");
TAP_TEST(state_g->transitions[G] == state_g, TEST_AC_TRANSITIONS, "");
TAP_TEST(state_g->transitions[C]->transitions[C] == state_c, TEST_AC_TRANSITIONS, "");
TAP_TEST(state_cag->transitions[G] == state_g, TEST_AC_TRANSITIONS, "");
TAP_TEST(state_cag->transitions[A]->is_final, TEST_AC_FINAL, "");
string caga = "caga";
string caca = "caca";
string acag = "acag";
TAP_TEST(aho.get(caga).count == 2, TEST_AC_GET, "");
TAP_TEST(aho.get(caca).count == 3, TEST_AC_GET, "");
TAP_TEST(aho.get(acag).count == 5, TEST_AC_GET, "");
}
void testFastaOutputOperator(){
ostringstream oss;
Fasta fa("../../data/test1.fa");
oss << fa;
TAP_TEST(oss.str() == ">seq1\nACAAC\n>seq2\nCGACCCCCAA\n>seq3\nA\n>seq4\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n>\nAATN\n", TEST_FASTA_OUT, oss.str());
}
void testRevcompInt() {
TAP_TEST(revcomp_int(dna_to_int("AA", 2), 2) == dna_to_int("TT", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("AC", 2), 2) == dna_to_int("GT", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("AG", 2), 2) == dna_to_int("CT", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("AT", 2), 2) == dna_to_int("AT", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("CA", 2), 2) == dna_to_int("TG", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("CC", 2), 2) == dna_to_int("GG", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("CG", 2), 2) == dna_to_int("CG", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("CT", 2), 2) == dna_to_int("AG", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("GA", 2), 2) == dna_to_int("TC", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("GC", 2), 2) == dna_to_int("GC", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("GT", 2), 2) == dna_to_int("AC", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("TA", 2), 2) == dna_to_int("TA", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("TC", 2), 2) == dna_to_int("GA", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("TG", 2), 2) == dna_to_int("CA", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("TT", 2), 2) == dna_to_int("AA", 2),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("AAAAAAA", 7), 7) == dna_to_int("TTTTTTT", 7),
TEST_REVCOMP_INT, "");
TAP_TEST(revcomp_int(dna_to_int("ATTAGGA", 7), 7) == dna_to_int("TCCTAAT", 7),
TEST_REVCOMP_INT, "revcomp: " << revcomp_int(dna_to_int("ATTAGGA", 7), 7) <<", dna_to_int: " << dna_to_int("TCCTAAT", 7));
}
void testDNAToInt() {
TAP_TEST(dna_to_int("A", 1) == 0, TEST_DNA_TO_INT, "");
TAP_TEST(dna_to_int("AAAAAAA", 7) == 0, TEST_DNA_TO_INT, "");
TAP_TEST(dna_to_int("ATTAGGA", 7) == 3880, TEST_DNA_TO_INT, "");
TAP_TEST(dna_to_int("TTTT", 4) == 255, TEST_DNA_TO_INT, "");
}
void testNucToInt() {
TAP_TEST(nuc_to_int('A') == 0, TEST_NUC_TO_INT, "");
TAP_TEST(nuc_to_int('C') == 1, TEST_NUC_TO_INT, "");
TAP_TEST(nuc_to_int('G') == 2, TEST_NUC_TO_INT, "");
TAP_TEST(nuc_to_int('T') == 3, TEST_NUC_TO_INT, "");
}
void testRevcomp() {
TAP_TEST(complement("AATCAGactgactagATCGAn") == "TTAGTCTGACTGATCTAGCTN", TEST_REVCOMP, "");
TAP_TEST(revcomp("AATCAGactgactagATCGAn") == "NTCGATCTAGTCAGTCTGATT", TEST_REVCOMP, "");
TAP_TEST(revcomp("") == "", TEST_REVCOMP, "");
TAP_TEST(revcomp("aaaaaa") == "TTTTTT", TEST_REVCOMP, "");
}