readFasta.h

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/*
    Copyright (C) 2011 Laszlo Kajan, Technical University of Munich, Germany
 
    This file is part of librostlab.
 
    librostlab is free software: you can redistribute it and/or modify
    it under the terms of the GNU Lesser 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 Lesser General Public License for more details.
 
    You should have received a copy of the GNU Lesser General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef ROSTLAB_READFASTA
#define ROSTLAB_READFASTA 1
 
#include <boost/regex.hpp>
#include <iostream>
#include <fstream>
#include "rostlab/rostlab_stdexcept.h"
 
namespace bo = boost;
 
namespace rostlab {
namespace bio {
 
  namespace fmt {
    class fasta{}; // fasta format class
  };
 
template<typename _FmtT>
class seq {
  private:
    std::string        _desc;
    std::string        _display_id;
    std::string        _seqstr;
  public:
                  seq(){};
                  seq( const std::string& __desc, const std::string& __display_id, const std::string& __seqstr ) : _desc(__desc), _display_id(__display_id), _seqstr(__seqstr) {};
    virtual       ~seq(){};
 
    std::string&       seqstr(){ return _seqstr; };
};
 
/*template<> // could specialize it...
class seq<bio::fmt::fasta>
{
  private:
  public:
};*/
 
/*template<typename _FmtT>
std::istream&          operator>>( std::istream& __is, bio::seq<_FmtT>& __n )
{
  return __is;
}*/
 
inline std::istream&   operator>>( std::istream& __is, bio::seq<bio::fmt::fasta>& __seq )
{
  // based on Bio/SeqIO/fasta.pm
  std::string rec; rec.reserve(1024);
  while( __is.peek() != std::istream::traits_type::eof() )
  {
    if(rec.capacity() == rec.size()) rec.reserve(rec.capacity() * 2);
    if( rec.size() && __is.peek() == '>' && *rec.rbegin() == '\n' ) break;
    else rec += __is.get();
  }
 
  if( !rec.size() || *rec.begin() != '>' ) throw runtime_error( std::string("FASTA syntax error in record '") + rec + "': no leading '>'" );
 
  rec = bo::regex_replace( rec, bo::regex("^>"), "" ); // $entry =~ s/^>//;
 
  bo::sregex_token_iterator i(rec.begin(), rec.end(), bo::regex("\n"), -1); // split(/\n/,$entry,2);
 
  if( i == boost::sregex_token_iterator() ) throw runtime_error( std::string("FASTA syntax error in record '") + rec + "': only one line" );
 
  std::string top = *i++;
  std::string sequence( i->first, static_cast<std::string::const_iterator>( rec.end() ) );
 
  sequence = bo::regex_replace( sequence, bo::regex(">"), "" ); // $sequence =~ s/>//g;
 
  bo::match_results<std::string::const_iterator> what;
  std::string id, fulldesc;
  if( bo::regex_search( top, what, bo::regex("^[[:space:]]*([^[:space:]]+)[:space:]*(.*)") ) )
  { id = std::string( what[1].first, what[1].second ); fulldesc = std::string( what[2].first, what[2].second ); }
 
  if( id.empty() ) id = fulldesc;
 
  sequence = bo::regex_replace( sequence, bo::regex("[ \t\n\r]"), "" );
 
  // alphabet? would be good to have this
 
  __seq = bio::seq<bio::fmt::fasta>( fulldesc, id, sequence );
 
  return __is;
}
 
}; // namespace bio
}; // namespace rostlab
 
#endif /* ROSTLAB_READFASTA */
// vim:et:ts=2:ai: