I want to parse a file that looks like this (FASTA-like text format):
>InfoHeader
"Some text sequence that has a line break after every 80 characters"
>InfoHeader
"Some text sequence that has a line break after every 80 characters"
...
e.g.:
>gi|31563518|ref|NP_852610.1| microtubule-associated proteins 1A/1B light chain 3A isoform b [Homo sapiens]
MKMRFFSSPCGKAAVDPADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKI
IRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKDEDGFLYMVYASQETFGFIRENE
I wrote a parser for this with boost::spirit. The parser correctly stores the header line and the following text sequence in a std::vector< std::pair< string, string >> but it takes kind of long for bigger files (17sec for a 100MB file). As comparison I wrote a program without boost::spirit (just STL functions) that simply copies each line of that 100MB file in a std::vector. The whole process takes less than a second. The "program" used for the comparison is not serving the purpose but I don't think the parser should take that much longer...
I know there are plenty of other FASTA parsers around but I'm rather curious why my code is slow.
The .hpp file:
#include <boost/filesystem/path.hpp>
namespace fs = boost::filesystem;
class FastaReader {
public:
typedef std::vector< std::pair<std::string, std::string> > fastaVector;
private:
fastaVector fV;
fs::path file;
public:
FastaReader(const fs::path & f);
~FastaReader();
const fs::path & getFile() const;
const fastaVector::const_iterator getBeginIterator() const;
const fastaVector::const_iterator getEndIterator() const;
private:
void parse();
};
And the .cpp file:
#include <iomanip>
#include <boost/date_time/posix_time/posix_time.hpp>
#include <boost/filesystem/fstream.hpp>
#include <boost/filesystem/operations.hpp>
#include <boost/filesystem/path.hpp>
#include <boost/spirit/include/classic_position_iterator.hpp>
#include <boost/spirit/include/phoenix_bind.hpp>
#include <boost/spirit/include/phoenix_core.hpp>
#include <boost/spirit/include/phoenix_fusion.hpp>
#include <boost/spirit/include/phoenix_operator.hpp>
#include <boost/spirit/include/qi.hpp>
#include "fastaReader.hpp"
using namespace std;
namespace fs = boost::filesystem;
namespace qi = boost::spirit::qi;
namespace pt = boost::posix_time;
template <typename Iterator, typename Skipper>
struct FastaGrammar : qi::grammar<Iterator, FastaReader::fastaVector(), qi::locals<string>, Skipper> {
qi::rule<Iterator> infoLineStart;
qi::rule<Iterator> inputEnd;
qi::rule<Iterator> lineEnd;
qi::rule<Iterator, string(), Skipper> infoLine;
qi::rule<Iterator, string(), Skipper> seqLine;
qi::rule<Iterator, FastaReader::fastaVector(), qi::locals<string>, Skipper> fasta;
FastaGrammar() : FastaGrammar::base_type(fasta, "fasta") {
using boost::spirit::standard::char_;
using boost::phoenix::bind;
using qi::eoi;
using qi::eol;
using qi::lexeme;
using qi::_1;
using qi::_val;
using namespace qi::labels;
infoLineStart = char_('>');
inputEnd = eoi;
/* grammar */
infoLine = lexeme[*(char_ - eol)];
seqLine = *(char_ - infoLineStart);
fasta = *(infoLineStart > infoLine[_a = _1]
> seqLine[bind(&FastaGrammar::addValue, _val, _a, _1)]
)
> inputEnd
;
infoLineStart.name(">");
infoLine.name("sequence identifier");
seqLine.name("sequence");
}
static void addValue(FastaReader::fastaVector & fa, const string & info, const string & seq) {
fa.push_back(make_pair(info, seq));
}
};
FastaReader::FastaReader(const fs::path & f) {
this->file = f;
this->parse();
}
FastaReader::~FastaReader() {}
const fs::path & FastaReader::getFile() const {
return this->file;
}
const FastaReader::fastaVector::const_iterator FastaReader::getBeginIterator() const {
return this->fV.cbegin();
}
const FastaReader::fastaVector::const_iterator FastaReader::getEndIterator() const {
return this->fV.cend();
}
void FastaReader::parse() {
if ( this->file.empty() ) throw string("FastaReader: No file specified.");
if ( ! fs::is_regular_file(this->file) ) throw (string("FastaReader: File not found: ") + this->file.string());
typedef boost::spirit::istream_iterator iterator_type;
typedef boost::spirit::classic::position_iterator2<iterator_type> pos_iterator_type;
typedef FastaGrammar<pos_iterator_type, boost::spirit::ascii::space_type> fastaGr;
fs::ifstream fin(this->file);
if ( ! fin.is_open() ) {
throw (string("FastaReader: Access denied: ") + this->file.string());
}
fin.unsetf(ios::skipws);
iterator_type begin(fin);
iterator_type end;
pos_iterator_type pos_begin(begin, end, this->file.string());
pos_iterator_type pos_end;
fastaGr fG;
try {
std::cerr << "Measuring: Parsing." << std::endl;
const pt::ptime startMeasurement = pt::microsec_clock::universal_time();
qi::phrase_parse(pos_begin, pos_end, fG, boost::spirit::ascii::space, this->fV);
const pt::ptime endMeasurement = pt::microsec_clock::universal_time();
pt::time_duration duration (endMeasurement - startMeasurement);
std::cerr << duration << std::endl;
} catch (std::string str) {
cerr << "error message: " << str << endl;
}
}
So the grammar does the folloing:
It looks for a ">" sign and then stores all following characters until an EOL is detected. After the EOL the text sequence starts and ends when a ">" sign is detected. Both strings (header line and text sequence) are then stored in a std::vector by calling FastaReader::addValue().
I compiled my program using g++ version 4.8.2 with -O2 and -std=c++11 flags.
So where is the the performance issue in my code?
Previous: Step 3: MOAR FASTER WITH ZERO-COPY
Return to Step 1. Cleaning up + Profiling
Since you're not using it, we can drop the stateful iterator, which is likely to inhibit quite a lot of optimizations (and was indirectly visible in the profiler output)
#define BOOST_SPIRIT_USE_PHOENIX_V3
#include <boost/filesystem/path.hpp>
#include <boost/utility/string_ref.hpp>
#include <boost/iostreams/device/mapped_file.hpp>
namespace io = boost::iostreams;
namespace fs = boost::filesystem;
class FastaReader {
public:
typedef std::pair<boost::string_ref, boost::string_ref> Entry;
typedef std::vector<Entry> Data;
private:
Data fV;
fs::path file;
public:
FastaReader(const fs::path & f);
~FastaReader();
const fs::path & getFile() const;
const Data::const_iterator begin() const;
const Data::const_iterator end() const;
private:
io::mapped_file_source mmap;
void parse();
};
#include <iomanip>
#include <boost/date_time/posix_time/posix_time.hpp>
#include <boost/filesystem/fstream.hpp>
#include <boost/filesystem/operations.hpp>
#include <boost/filesystem/path.hpp>
#include <boost/spirit/include/qi.hpp>
#include <boost/spirit/include/phoenix.hpp>
#include <boost/fusion/adapted/std_pair.hpp>
//#include "fastaReader.hpp"
#include <boost/iostreams/device/mapped_file.hpp>
using namespace std;
namespace fs = boost::filesystem;
namespace qi = boost::spirit::qi;
namespace pt = boost::posix_time;
namespace io = boost::iostreams;
namespace boost { namespace spirit { namespace traits {
template <typename It>
struct assign_to_attribute_from_iterators<boost::string_ref, It, void> {
static void call(It f, It l, boost::string_ref& attr) { attr = boost::string_ref { f, size_t(std::distance(f,l)) }; }
};
} } }
template <typename Iterator>
struct FastaGrammar : qi::grammar<Iterator, FastaReader::Data()> {
FastaGrammar() : FastaGrammar::base_type(fasta) {
using namespace qi;
using boost::phoenix::construct;
using boost::phoenix::begin;
using boost::phoenix::size;
entry = ('>' >> raw[ *~char_('\n') ] >> '\n' >> raw[ *~char_('>') ]);
fasta = *entry >> *eol >> eoi ;
BOOST_SPIRIT_DEBUG_NODES((fasta)(entry));
}
private:
qi::rule<Iterator, FastaReader::Data()> fasta;
qi::rule<Iterator, FastaReader::Entry()> entry;
};
FastaReader::FastaReader(const fs::path & f) : file(f), mmap(file.c_str()) {
parse();
}
FastaReader::~FastaReader() {}
const fs::path & FastaReader::getFile() const {
return this->file;
}
const FastaReader::Data::const_iterator FastaReader::begin() const {
return this->fV.cbegin();
}
const FastaReader::Data::const_iterator FastaReader::end() const {
return this->fV.cend();
}
void FastaReader::parse() {
if (this->file.empty()) throw std::runtime_error("FastaReader: No file specified.");
if (! fs::is_regular_file(this->file)) throw std::runtime_error(string("FastaReader: File not found: ") + this->file.string());
typedef char const* iterator_type;
typedef FastaGrammar<iterator_type> fastaGr;
static const fastaGr fG{};
try {
std::cerr << "Measuring: Parsing." << std::endl;
const pt::ptime startMeasurement = pt::microsec_clock::universal_time();
iterator_type first(mmap.data()), last(mmap.end());
qi::phrase_parse(first, last, fG, boost::spirit::ascii::space, this->fV);
const pt::ptime endMeasurement = pt::microsec_clock::universal_time();
pt::time_duration duration (endMeasurement - startMeasurement);
std::cerr << duration << std::endl;
} catch (std::exception const& e) {
cerr << "error message: " << e.what() << endl;
}
}
int main() {
FastaReader reader("input.txt");
for (auto& e : reader) std::cout << '>' << e.first << '\n' << e.second << "\n\n";
}
Now it's 74.8x faster.
$ time ./test | head -n4
Measuring: Parsing.
00:00:00.194432