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/*
* Copyright (C) 2011 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include <getopt.h>
#include "Generic.h"
#include <stdio.h>
#include "ReferenceSequence.h"
#include "UnitTest.h"
#include <assert.h>
#include <sstream>
class ReferenceSequenceTest : public UnitTest
{
public:
ReferenceSequenceTest(const char *title) : UnitTest(title) {;}
void test1();
void test2();
void test3();
void humanGenomeTest1();
void test() {
test1();
test2();
test3();
// This test is very slow:
// humanGenomeTest1();
}
};
void ReferenceSequenceTest::test1(void)
{
std::string sequence("ACTGACTGACTGACTGACTGACTGACTGACTGACTGACTG");
std::string word;
word="ACTG";
check(m_failures, ++m_testNum, "Test wordMatch with std::string", true,
Sequence::wordMatch(sequence, 4, word));
std::stringstream output;
Sequence::printNearbyWords(output, sequence, 8, word, 4);
std::string expect("\
word 'ACTG' found -4 away from position 8.\n\
word 'ACTG' found 0 away from position 8.\n\
");
check(m_failures, ++m_testNum, "Test printNearbyWords with std::string", expect, output.str());
Sequence::getString(sequence, 4, 4, word);
check(m_failures, ++m_testNum, "Test getString with std::string", "ACTG", word);
Sequence::getHighLightedString(sequence, 0, 12, word, 4, 8);
check(m_failures, ++m_testNum, "Test getHighLightedStribng with std::string", "ACTGactgACTG",word);
#if 0
// busted test - don't know why
output.clear();
output.str(std::string());
// Sequence::printBaseContext(std::cout, sequence, 8, 4);
Sequence::printBaseContext(output, sequence, 8, 4);
expect="\
index: 8\n\
ACTGACTGA\n\
^\n\
";
check(m_failures, ++m_testNum, "Test printBaseContext with std::string", expect, output.str());
#endif
std::string result;
std::string read("ACTGZZZZACTG");
expect = " ^^^^ ";
Sequence::getMismatchHatString(sequence, 4, result, read);
check(m_failures, ++m_testNum, "Test getMismatchHatString with std::string", expect, result);
read="ACTG";
std::string quality("");
size_t location = Sequence::simpleLocalAligner(sequence, 0, read, quality, 12);
check(m_failures, ++m_testNum, "Test simpleLocalAligner with std::string", (size_t) 0, location);
read="ACNG";
int misMatches = Sequence::getMismatchCount(sequence, 0, read);
check(m_failures, ++m_testNum, "Test getMismatchCount with std::string", 1, misMatches);
read="ACNG";
quality="$$$$";
int sumQ = Sequence::getSumQ(sequence, 0, read, quality);
check(m_failures, ++m_testNum, "Test getSumQ with std::string", 3, sumQ);
}
void ReferenceSequenceTest::test2(void)
{
PackedSequenceData sequence;
std::string word;
sequence.push_back('A');
sequence.push_back('C');
sequence.push_back('T');
sequence.push_back('G');
sequence.push_back('A');
sequence.push_back('C');
sequence.push_back('T');
sequence.push_back('G');
sequence.push_back('A');
sequence.push_back('C');
sequence.push_back('T');
sequence.push_back('G');
sequence.push_back('A');
sequence.push_back('C');
sequence.push_back('T');
sequence.push_back('G');
Sequence::getString(sequence, 4, 4, word);
check(m_failures, ++m_testNum, "Test getString with PackedSequenceData", "ACTG", word);
std::cout << "test2 sequence utilization is " << sequence.getUtilization() * 100 << "% - expect around 6.25%" << std::endl;
}
void ReferenceSequenceTest::test3(void)
{
std::vector<PackedSequenceData> chromosomeSequence;
std::vector<std::string> chromosomeNames;
bool result = loadFastaFile("../phiX.fa", chromosomeSequence, chromosomeNames);
if(result) {
std::cout << "../phiX.fa not found - skipping these tests." << std::endl;
return;
}
std::cout << "phiX reference utilization is " << chromosomeSequence[0].getUtilization() * 100 << "% - expect around 96.8%" << std::endl;
check(m_failures, ++m_testNum, "Test loadFastaFile with PackedSequenceData", (size_t) 1, chromosomeNames.size());
check(m_failures, ++m_testNum, "Test loadFastaFile with PackedSequenceData", (size_t) 1, chromosomeSequence.size());
check(m_failures, ++m_testNum, "Test loadFastaFile with PackedSequenceData", "1", chromosomeNames[0]);
std::string word;
Sequence::getString(chromosomeSequence[0], 60, 10, word);
check(m_failures, ++m_testNum, "Test loadFastaFile with PackedSequenceData", "AAATTATCTT", word);
}
void ReferenceSequenceTest::humanGenomeTest1(void)
{
std::vector<PackedSequenceData> chromosomeSequence;
std::vector<std::string> chromosomeNames;
#define HUMAN_GENOME "/data/local/ref/karma.ref/human.g1k.v37.fa"
bool result = loadFastaFile(HUMAN_GENOME, chromosomeSequence, chromosomeNames);
if(result) {
std::cout << HUMAN_GENOME << " not found - skipping these tests." << std::endl;
return;
}
}
int main(int argc, char **argv)
{
ReferenceSequenceTest test("ReferenceSequenceTest");
test.test();
std::cout << test;
exit(test.getFailureCount());
}
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