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#include <fstream>
#include <gtest/gtest.h>
#include <jellyfish/whole_sequence_parser.hpp>
#include <unit_tests/test_main.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::whole_sequence_parser<opened_streams<std::ifstream**> > parser_type;
TEST(SequenceParser, Fasta) {
static const char* seq1 = "ATTACCTTGTACCTTCAGAGC";
static const char* seq2 = "TTCGATCCCTTGATAATTAGTCACGTTAGCT";
const char* file_name = "Fasta.fa";
file_unlink fu(file_name);
{
std::ofstream sequence(file_name);
sequence << ">header1\n"
<< seq1 << "\n\n"
<< ">header2\n"
<< seq2 << "\n\n\n"
<< seq1;
}
auto sequence = new std::ifstream(file_name);
opened_streams<std::ifstream**> streams(&sequence, &sequence + 1);
parser_type parser(10, 1, 1, streams);
{
parser_type::job j(parser);
ASSERT_FALSE(j.is_empty());
ASSERT_EQ((size_t)1, j->nb_filled);
EXPECT_STREQ("header1", j->data[0].header.c_str());
EXPECT_STREQ(seq1, j->data[0].seq.c_str());
}
{
parser_type::job j(parser);
ASSERT_FALSE(j.is_empty());
ASSERT_EQ((size_t)1, j->nb_filled);
EXPECT_STREQ("header2", j->data[0].header.c_str());
EXPECT_EQ(strlen(seq2) + strlen(seq1), j->data[0].seq.size());
EXPECT_STREQ(seq2, j->data[0].seq.substr(0, strlen(seq2)).c_str());
EXPECT_STREQ(seq1, j->data[0].seq.substr(strlen(seq2)).c_str());
}
{
parser_type::job j(parser);
EXPECT_TRUE(j.is_empty());
}
EXPECT_EQ((size_t)1, parser.nb_files());
EXPECT_EQ((size_t)2, parser.nb_reads());
}
TEST(SequenceParser, Fastq) {
static const char* seq1 = "ATTACCTTGTACCTTCAGAGC";
static const char* seq2 = "TTCGATCCCTTGATAATTAGTCACGTTAGCT";
const char* file_name = "Fasta.fq";
file_unlink fu(file_name);
{
std::ofstream sequence(file_name);
sequence << "@header1\n"
<< seq1 << "\n\n"
<< "+and some stuff\n"
<< seq1 << "\n"
<< "@header2\n"
<< seq2 << "\n\n\n"
<< seq1 << "\n"
<< "+\n"
<< seq1 << "\n"
<< seq2 << "\n";
}
auto sequence = new std::ifstream(file_name);
opened_streams<std::ifstream**> streams(&sequence, &sequence + 1);
parser_type parser(10, 1, 1, streams);
{
parser_type::job j(parser);
ASSERT_FALSE(j.is_empty());
ASSERT_EQ((size_t)1, j->nb_filled);
EXPECT_STREQ("header1", j->data[0].header.c_str());
EXPECT_STREQ(seq1, j->data[0].seq.c_str());
EXPECT_STREQ(seq1, j->data[0].qual.c_str());
}
{
parser_type::job j(parser);
ASSERT_FALSE(j.is_empty());
ASSERT_EQ((size_t)1, j->nb_filled);
EXPECT_STREQ("header2", j->data[0].header.c_str());
EXPECT_EQ(strlen(seq2) + strlen(seq1), j->data[0].seq.size());
EXPECT_EQ(strlen(seq2) + strlen(seq1), j->data[0].qual.size());
EXPECT_STREQ(seq2, j->data[0].seq.substr(0, strlen(seq2)).c_str());
EXPECT_STREQ(seq1, j->data[0].seq.substr(strlen(seq2)).c_str());
EXPECT_STREQ(seq1, j->data[0].qual.substr(0, strlen(seq1)).c_str());
EXPECT_STREQ(seq2, j->data[0].qual.substr(strlen(seq1)).c_str());
}
{
parser_type::job j(parser);
EXPECT_TRUE(j.is_empty());
}
EXPECT_EQ((size_t)1, parser.nb_files());
EXPECT_EQ((size_t)2, parser.nb_reads());
}
TEST(SequenceParser, FastaMany) {
const char* file_name = "FastaMany.fa";
file_unlink fu(file_name);
static const int nb_sequences = 1000;
{
std::ofstream sequence(file_name);
ASSERT_TRUE(sequence.good());
for(int i = 0; i < nb_sequences; ++i) {
const int seq_len = random_bits(8) + 10;
sequence << ">" << i << " " << seq_len << "\n";
for(int j = 0; j < seq_len; ++j) {
sequence << (char)('A' + j % 26);
if(random_bits(6) == 0)
sequence << '\n';
}
sequence << '\n';
}
}
auto sequence = new std::ifstream(file_name);
opened_streams<std::ifstream**> streams(&sequence, &sequence + 1);
parser_type parser(10, 13, 1, streams);
int got_sequences = 0;
while(true) {
parser_type::job job(parser);
if(job.is_empty())
break;
for(size_t i = 0; i < job->nb_filled; ++i) {
++got_sequences;
const size_t len_pos = job->data[i].header.find_first_of(" ");
const int seq_len = atoi(job->data[i].header.c_str() + len_pos + 1);
ASSERT_LE(10, seq_len);
for(int j = 0; j < seq_len; ++j)
EXPECT_EQ('A' + (j % 26), job->data[i].seq[j]);
}
}
EXPECT_EQ(nb_sequences, got_sequences);
EXPECT_EQ((size_t)1, parser.nb_files());
EXPECT_EQ((size_t)nb_sequences, parser.nb_reads());
}
}
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