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/**
>HEADER
Copyright (c) 2013 Rob Patro robp@cs.cmu.edu
This file is part of Sailfish.
Sailfish 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.
Sailfish 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 Sailfish. If not, see <http://www.gnu.org/licenses/>.
<HEADER
**/
#ifndef GENOMIC_FEATURE_HPP
#define GENOMIC_FEATURE_HPP
#include <boost/thread/thread.hpp>
#include <atomic>
#include <thread>
#include <fstream>
#include <boost/tokenizer.hpp>
#include "tbb/concurrent_queue.h"
struct TranscriptGeneID {
std::string transcript_id;
std::string gene_id;
// std::unordered_map<std::string, std::string> dynamic;
bool parseAttribute( std::string& key, std::string& val ) {
if ( key == "transcript_id" ) { transcript_id = val; return true; }
if ( key == "gene_id" ) { gene_id = val; return true; }
// dynamic[key] = val;
return false;
}
};
std::ostream& operator<< ( std::ostream& out, const TranscriptGeneID& ids );
template< typename StaticAttributes >
class GenomicFeature {
public:
std::string seqID;
std::string source;
std::string type;
int start, end;
float score;
char strand;
char phase;
StaticAttributes sattr;
template <typename T>
friend std::ostream& operator<< ( std::ostream& out, const GenomicFeature<T>& gf );
template <typename T>
friend std::istream& operator>> ( std::istream& in, const GenomicFeature<T>& gf );
};
template< typename StaticAttributes>
std::ostream& operator<< ( std::ostream& out, const GenomicFeature<StaticAttributes>& gf );
template< typename StaticAttributes >
std::istream& operator>> ( std::istream& in, GenomicFeature<StaticAttributes>& gf );
namespace GTFParser {
template< typename CustomGenomicFeature >
void genomicFeatureFromLine( std::string& l, CustomGenomicFeature& gf ) {
size_t head = 0;
size_t tail = l.find_first_of('\t');
gf.seqID = l.substr(head,tail);
head = tail+1;
tail = l.find_first_of('\t', head);
gf.source = l.substr(head, tail-head);
head = tail+1;
tail = l.find_first_of('\t', head);
gf.type = l.substr(head, tail-head);
head = tail+1;
tail = l.find_first_of('\t', head);
gf.start = atoi(l.substr(head, tail-head).c_str());
head = tail+1;
tail = l.find_first_of('\t', head);
gf.end = atoi(l.substr(head, tail-head).c_str());
head = tail+1;
tail = l.find_first_of('\t', head);
gf.score = atoi(l.substr(head, tail-head).c_str());
head = tail+1;
tail = l.find_first_of('\t', head);
gf.strand = l.substr(tail, tail-head)[0];
head = tail+1;
tail = l.find_first_of('\t', head);
gf.phase = l.substr(tail, tail-head)[0];
head = tail+1;
tail = l.find_first_of('\n', head);
auto line = l.substr(head, tail-head);
using tokenizer = boost::tokenizer<boost::char_separator<char>>;
boost::char_separator<char> sep(";");
tokenizer tokens(line, sep);
for ( auto tokIt : tokens ) {
// Currently, we'll handle the following separators
// '\s+'
// '\s*=\s*'
tokIt = tokIt.substr(tokIt.find_first_not_of(' '));
auto kvsepStart = tokIt.find('=');
// If we reached the end of the key, value token, then the string must have been
// separated by some set of spaces, and NO '='. If this is the case, find the 'spaces' so that
// we can split on it.
if ( kvsepStart == tokIt.npos ) {
kvsepStart = tokIt.find(' ');
}
auto key = tokIt.substr(0, kvsepStart);
key = key.substr(0, key.find(' '));
auto kvsepStop = 1 + kvsepStart + tokIt.substr(kvsepStart+1).find_first_not_of(' ');
auto val = (tokIt[kvsepStop] == '"') ? tokIt.substr(kvsepStop+1, (tokIt.length() - (kvsepStop+2))) : tokIt.substr(kvsepStop, (tokIt.length() - (kvsepStop+1)));
gf.sattr.parseAttribute( key, val );
}
}
template <typename StaticAttributes>
std::vector<GenomicFeature<StaticAttributes>> readGTFFile( const std::string& fname ) {
using StringPtr = std::string*;
std::vector<GenomicFeature<StaticAttributes>> feats;
std::ifstream ifile(fname);
bool done = false;
std::vector<std::thread> threads;
tbb::concurrent_queue<StringPtr> queue;
//boost::lockfree::queue<StringPtr> queue(5000);
threads.push_back(
std::thread([&ifile, &queue, &done]() {
StringPtr line = new std::string();
while( !std::getline(ifile, *line).eof() ) {
StringPtr ownedLine = line;
queue.push(ownedLine);
// for boost lockfree
// while( !queue.push(ownedLine) ) {}
line = new std::string();
}
done = true;
})
);
size_t nreader=10;
std::atomic<size_t> tctr(nreader);
tbb::concurrent_queue<GenomicFeature<StaticAttributes>*> outQueue;
// boost::lockfree::queue<GenomicFeature<StaticAttributes>*> outQueue(5000);
for( size_t i = 0; i < nreader; ++i ) {
threads.push_back(
std::thread([&queue, &outQueue, &done, &tctr]() -> void {
StringPtr l = nullptr;
while( !done or queue.try_pop(l) ) {
if ( l != nullptr ) {
auto gf = new GenomicFeature<StaticAttributes>();
genomicFeatureFromLine(*l, *gf);
outQueue.push(gf);
// for boost lockfree
// while( !outQueue.push(gf) ) {}
delete l;
l = nullptr;
}
}
--tctr;
}
));
}
threads.push_back(
std::thread([&outQueue, &feats, &tctr]() -> void {
GenomicFeature<StaticAttributes>* f = nullptr;
while( outQueue.try_pop(f) or tctr > 0 ) {
if ( f != nullptr ) {
feats.push_back(*f);
}
}
}
));
// Wait for all of the threads to finish
for ( auto& thread : threads ){ thread.join(); }
ifile.close();
return feats;
}
}
#endif // GENOMIC_FEATURE_HPP
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