fasta.cpp 6.83 KB
Newer Older
Mikaël Salson's avatar
Mikaël Salson committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
/*
  This file is part of "Vidjil" <http://bioinfo.lifl.fr/vid>
  Copyright (C) 2011, 2012, 2013 by Bonsai bioinformatics at LIFL (UMR CNRS 8022, Université Lille) and Inria Lille
  Contributors: Mathieu Giraud <mathieu.giraud@lifl.fr>, Mikaël Salson <mikael.salson@lifl.fr>, David Chatel

  "Vidjil" 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.

  "Vidjil" 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 "Vidjil". If not, see <http://www.gnu.org/licenses/>
*/

#include <fstream>
#include <iostream>
#include <iomanip>
#include <algorithm>
#include <cctype>
#include <stdexcept>
#include "fasta.h"

Fasta::Fasta(){
}

Fasta::Fasta(const string &input, 
	     int extract_field, string extract_separator,
	     ostream &out) 
{
  if (!input.size()) // Do not open empty files (D germline if not segmentD)
    return ;

  // oout = out;
  this -> extract_field = extract_field ;
  this -> extract_separator = extract_separator ;
41
  total_size = 0;
Mikaël Salson's avatar
Mikaël Salson committed
42

43
  add(input);  
Mikaël Salson's avatar
Mikaël Salson committed
44

45 46 47 48 49 50 51 52 53 54
  out << "  <== " << input
      << "\t" << setw(6) << total_size << " bp in " << setw(3) << size() << " sequences" << endl ;
}

void Fasta::add(istream &in) {
  in >> *this;
}

void Fasta::add(const string &filename) {
  ifstream is(filename.c_str());
Mikaël Salson's avatar
Mikaël Salson committed
55 56
  if (is.fail())
    {
57
      cerr << "  !! Error in opening file: " << filename << endl ;
Mikaël Salson's avatar
Mikaël Salson committed
58 59
      exit(1);
    }
60
  add(is);
Mikaël Salson's avatar
Mikaël Salson committed
61 62 63 64
  is.close();
}

int Fasta::size() const{ return (int)reads.size(); }
Mathieu Giraud's avatar
Mathieu Giraud committed
65 66 67 68 69 70 71 72 73
list<Sequence> Fasta::getAll() const {
  list<Sequence> reads;

  for (int i=0; i < size(); i++) {
    reads.push_back(read(i));
  }

  return reads;
}
Mikaël Salson's avatar
Mikaël Salson committed
74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92
const string& Fasta::label(int index) const{ return reads[index].label; }
const string& Fasta::label_full(int index) const{ return reads[index].label_full; }
const Sequence& Fasta::read(int index) const {return reads[index];}
const string& Fasta::sequence(int index) const{ return reads[index].sequence; }

// OnlineFasta

OnlineFasta::OnlineFasta(int extract_field, string extract_separator):
  input(NULL), extract_field(extract_field), extract_separator(extract_separator){}

OnlineFasta::OnlineFasta(const string &input, 
                         int extract_field, string extract_separator)
  :input(new ifstream(input.c_str())), 
  extract_field(extract_field), 
  extract_separator(extract_separator)
{
  if (this->input->fail()) {
    throw ios_base::failure("!! Error in opening file "+input);
  }
Mathieu Giraud's avatar
Mathieu Giraud committed
93 94

  cout << "  <== " << input << endl ;
Mikaël Salson's avatar
Mikaël Salson committed
95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121
  input_allocated = true;
  init();
}

OnlineFasta::OnlineFasta(istream &input, 
                         int extract_field, string extract_separator)
  :extract_field(extract_field), 
  extract_separator(extract_separator)
{
  this->input = &input;
  input_allocated = false;
  init();
}

OnlineFasta::OnlineFasta(const OnlineFasta &of) {
  current = of.current;
  input = of.input;
  extract_field = of.extract_field;
  extract_separator = of.extract_separator;
  line = of.line;
  input_allocated = false;
  line_nb = of.line_nb;
}

OnlineFasta::~OnlineFasta() {
  if (input_allocated)
    delete input;
122 123
  if (current.seq)
    delete [] current.seq;
Mikaël Salson's avatar
Mikaël Salson committed
124 125 126 127 128
}

void OnlineFasta::init() {
  line_nb = 0;
  line = getInterestingLine();
129
  current.seq = NULL;
Mikaël Salson's avatar
Mikaël Salson committed
130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151
}

size_t OnlineFasta::getLineNb() {
  return line_nb;
}

Sequence OnlineFasta::getSequence() {
  return current;
}

bool OnlineFasta::hasNext() {
  return (! input->eof()) || line.length() > 0;
}

void OnlineFasta::next() {
  fasta_state state = FASTX_UNINIT;

  // Reinit the Sequence object
  current.label_full.erase();
  current.label.erase();
  current.sequence.erase();
  current.quality.erase();
152 153
  if (current.seq)
    delete [] current.seq;
Mikaël Salson's avatar
Mikaël Salson committed
154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200

  if  (hasNext()) {
    switch(line[0]) {
    case '>': state=FASTX_FASTA; break;
    case '@': state=FASTX_FASTQ_ID; break;
    default: 
      throw runtime_error("The file seems to be malformed!");
    }
    
    // Identifier line
    current.label_full = line.substr(1);
    current.label = extract_from_label(current.label_full, extract_field, extract_separator);

    line = getInterestingLine();
    while (hasNext() && ((state != FASTX_FASTA || line[0] != '>')
                         && (state != FASTX_FASTQ_QUAL || line[0] != '@'))) {

      if (hasNext()) {
        switch(state) {
        case FASTX_FASTA: case FASTX_FASTQ_ID:
          // Sequence
          current.sequence += line;
          break;
        case FASTX_FASTQ_SEQ:
          // FASTQ separator between sequence and quality
          assert(line[0] == '+');
          break;
        case FASTX_FASTQ_SEP:
          // Reading quality
          current.quality = line;
          break;
        default:
          throw runtime_error("Unexpected state after reading identifiers line");
        }
        if (state >= FASTX_FASTQ_ID && state <= FASTX_FASTQ_SEP)
          state = (fasta_state)(((int)state) + 1);
      } else {
        unexpectedEOF();
      }
      line = getInterestingLine();
    }

    if (state >= FASTX_FASTQ_ID && state < FASTX_FASTQ_QUAL) 
      unexpectedEOF();

    // Sequence in uppercase
    transform(current.sequence.begin(), current.sequence.end(), current.sequence.begin(), (int (*)(int))toupper);
201 202 203

    // Compute seq
    current.seq = new int[current.sequence.length()];
204
    for (unsigned int i=0; i< current.sequence.length(); i++)
205
      {
206
	current.seq[i] = nuc_to_int(current.sequence[i]) ;
207 208
      }

Mikaël Salson's avatar
Mikaël Salson committed
209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262
  } else
    unexpectedEOF();
}

OnlineFasta& OnlineFasta::operator=(const OnlineFasta&of) {
  current = of.current;
  line = of.line;
  input = of.input;
  extract_field = of.extract_field;
  extract_separator = of.extract_separator;
  return *this;
}

string OnlineFasta::getInterestingLine() {
  string line;
  while (line.length() == 0 && hasNext() && getline(*input, line)) {
    line_nb++;
    remove_trailing_whitespaces(line);
  }
  return line;
}

void OnlineFasta::unexpectedEOF() {
  throw runtime_error("Unexpected EOF while reading FASTA/FASTQ file");
}

// Operators

istream& operator>>(istream& in, Fasta& fasta){
	string line;
	Sequence read;
        OnlineFasta of(in, fasta.extract_field, fasta.extract_separator);

        while (of.hasNext()) {
          of.next();
          fasta.reads.push_back(of.getSequence());
          fasta.total_size += of.getSequence().sequence.size();
        }
	return in;
}

ostream& operator<<(ostream& out, Fasta& fasta){
	for(int i = 0 ; i < fasta.size() ; i++){
          out << fasta.read(i) << endl;
	}
	return out;
}

ostream &operator<<(ostream &out, const Sequence &seq) {
  out << ">" << seq.label << endl;
  out << seq.sequence << endl;
  return out;
}