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#include <string>
#include <fstream>
#include <gtest/gtest.h>
#include <unit_tests/test_main.hpp>
#include <jellyfish/parser_common.hpp>
#include <jellyfish/mer_overlap_sequence_parser.hpp>
namespace {
using std::string;
using std::istringstream;
template<typename Iterator>
struct opened_streams {
Iterator begin_, end_;
opened_streams(Iterator begin, Iterator end) : begin_(begin), end_(end) { }
jellyfish::stream_type next() {
jellyfish::stream_type res;
if(begin_ != end_) {
res.standard.reset(*begin_);
++begin_;
}
return res;
}
};
typedef jellyfish::mer_overlap_sequence_parser<opened_streams<std::ifstream**> > parser_type;
static const char* line_endings[2] = {"\n", "\r\n"};
TEST(MerOverlapSequenceParser, OneSmallSequence) {
static const char* seq = "ATTACCTTGTACCTTCAGAGC";
const char* file_name = "OneSmallSequence.fa";
for(auto le : line_endings) {
file_unlink fu(file_name);
{ std::ofstream sequence(file_name);
sequence << ">header" << le << seq;
}
auto sequence = new std::ifstream(file_name);
opened_streams<std::ifstream**> streams(&sequence, &sequence + 1);
parser_type parser(10, 1, 10, 100, streams);
parser_type::job j(parser);
ASSERT_FALSE(j.is_empty());
EXPECT_EQ(strlen(seq), (size_t)(j->end - j->start));
EXPECT_STREQ(seq, j->start);
j.release();
parser_type::job j2(parser);
EXPECT_TRUE(j2.is_empty());
EXPECT_EQ((size_t)1, parser.nb_files());
EXPECT_EQ((size_t)1, parser.nb_reads());
}
}
string generate_sequences(std::ostream& os, int a, int b, int nb, const char* le, bool fastq = false) {
static const char bases[4] = {'A', 'C', 'G', 'T' };
string res;
for(int i = 0; i < nb; ++i) {
int len = a + random() % b;
os << (fastq ? "@" : ">") << "r" << i << " " << len << le;
for(int j = 0; j < len; ++j) {
char b = bases[random() & 0x3];
os << b;
res += b;
if(random() % 16 == 0)
os << le;
}
if(i != nb - 1)
res += 'N';
os << le;
if(fastq) {
os << '+' << le;
for(int j = 0; j < len; ++j) {
if(random() % 16 == 0)
os << le;
os << "#";
}
os << le;
}
}
return res;
}
TEST(MerOverlapSequenceParser, ManySmallSequences) {
const char* file_name = "ManySmallSequences.fa";
static const int nb_reads = 20;
static const int mer_len = 10;
for(auto le : line_endings) {
file_unlink fu(file_name);
std::ofstream o_sequence(file_name);
string res = generate_sequences(o_sequence, 20, 64, nb_reads, le);
o_sequence.close();
auto sequence = new std::ifstream(file_name);
opened_streams<std::ifstream**> streams(&sequence, &sequence + 1);
parser_type parser(mer_len, 1, 10, 100, streams);
size_t offset = 0;
while(true) {
parser_type::job j(parser);
if(j.is_empty())
break;
SCOPED_TRACE(::testing::Message() << offset << ": " << res.substr(offset, j->end - j->start));
EXPECT_EQ(res.substr(offset, j->end - j->start).c_str(), string(j->start, j->end - j->start));
offset += j->end - j->start - (mer_len - 1);
}
EXPECT_EQ(res.size(), offset + mer_len - 1);
EXPECT_EQ((size_t)1, parser.nb_files());
EXPECT_EQ((size_t)nb_reads, parser.nb_reads());
}
}
TEST(MerOverlapSequenceParser, BigSequences) {
const char* file_name1 = "BigSequences1.fa";
const char* file_name2 = "BigSequences2.fa";
for(auto le : line_endings) {
file_unlink fu1(file_name1);
file_unlink fu2(file_name2);
std::ofstream o_sequence(file_name1);
const string res0 = generate_sequences(o_sequence, 200, 100, 3, le);
o_sequence.close();
o_sequence.open(file_name2);
const string res1 = generate_sequences(o_sequence, 200, 100, 3, le);
o_sequence.close();
std::ifstream* tmps[2];
tmps[0] = new std::ifstream(file_name1);
tmps[1] = new std::ifstream(file_name2);
opened_streams<std::ifstream**> streams(tmps, tmps + 2);
static const int mer_len = 10;
parser_type parser(mer_len, 1, 10, 100, streams);
size_t offset = 0;
while(offset < res0.size() - mer_len + 1) {
parser_type::job j(parser);
ASSERT_FALSE(j.is_empty());
SCOPED_TRACE(::testing::Message() << offset << ": " << res0.substr(offset, j->end - j->start));
EXPECT_EQ(res0.substr(offset, j->end - j->start).c_str(), string(j->start, j->end - j->start));
offset += j->end - j->start - (mer_len - 1);
}
EXPECT_EQ(res0.size(), offset + mer_len - 1);
offset = 0;
while(offset < res1.size() - mer_len + 1) {
parser_type::job j(parser);
ASSERT_FALSE(j.is_empty());
SCOPED_TRACE(::testing::Message() << offset << ": " << res1.substr(offset, j->end - j->start));
EXPECT_EQ(res1.substr(offset, j->end - j->start).c_str(), string(j->start, j->end - j->start));
offset += j->end - j->start - (mer_len - 1);
}
EXPECT_EQ(res1.size(), offset + mer_len - 1);
parser_type::job j2(parser);
EXPECT_TRUE(j2.is_empty());
EXPECT_EQ((size_t)2, parser.nb_files());
EXPECT_EQ((size_t)6, parser.nb_reads());
}
}
TEST(MerOverlapSequenceParser, Fastq) {
const char* file_name = "Fastq.fa";
static const int nb_reads = 100;
static const int mer_len = 20;
for(auto le : line_endings) {
file_unlink fu(file_name);
std::ofstream o_sequence(file_name);
string res = generate_sequences(o_sequence, 10, 50, nb_reads, le, true);
o_sequence.close();
auto sequence = new std::ifstream(file_name);
opened_streams<std::ifstream**> streams(&sequence, &sequence + 1);
parser_type parser(mer_len, 1, 10, 100, streams);
size_t offset = 0;
while(true) {
parser_type::job j(parser);
if(j.is_empty())
break;
// SCOPED_TRACE(::testing::Message() << offset << ": " << res.substr(offset, j->end - j->start));
EXPECT_EQ(res.substr(offset, j->end - j->start).c_str(), string(j->start, j->end - j->start));
offset += j->end - j->start - (mer_len - 1);
}
EXPECT_EQ(res.size(), offset + mer_len - 1);
EXPECT_EQ((size_t)1, parser.nb_files());
EXPECT_EQ((size_t)nb_reads, parser.nb_reads());
}
}
} // namespace {
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