Exemple #1
0
fasta::SequenceList fasta::remove_gaps(
    const fasta::SequenceList& sequences) {
  auto s = sequences;
  for (auto& seq : s) {
    seq.residues.clear();
  }
  for (size_t i = 0; i < sequences.size(); ++i) {
    for (size_t j = 0; j < sequences[i].residues.size(); ++j) {
      if (sequences[i].residues[j].codon[0] != '-') {
        s[i].residues.push_back(sequences[i].residues[j]);
      }
    }
  }
  return s;
}
Exemple #2
0
bool fasta::check_length(fasta::SequenceList const& sequences, int limit) {
  if (limit == 0) {
    limit = sequences.size();
  }
  auto result = true;
  auto prev_length = sequences[0].residues.size();
  auto i = 1;
  while (result && i < limit) {
    auto length = sequences[i].residues.size();
    if (length != prev_length) {
      result = false;
    }
    ++i;
  }
  return result;
}
Exemple #3
0
std::unordered_map<std::string, Occurences> FeatureScores::update_occurences(
    const fasta::SequenceList& sequences,
    const std::vector<double>& identities, const bool fade_out) {

  std::unordered_map<std::string, Occurences> p;
  for (auto& f: m_features) {
    p[f] = std::vector<double>(sequences[0].residues.size(), 0);
  }

  for (size_t i = 0; i < sequences[0].residues.size(); ++i) {
    for (size_t j = 0; j < sequences.size(); ++j) {
      for (auto& f : sequences[j].residues[i].features) {
        assert(p.find(f) != p.end());
        if (fade_out) {
          p[f][i] += 0.5 * (1 + identities[j]);
        } else {
          p[f][i] += 1.0;
        }
      }
    }
  }
  return p;
}
Exemple #4
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void FeatureScores::update_scores(const fasta::SequenceList& sequences,
    const f_config::FeatureSettingsMap& f_set,
    const std::vector<double>& identities,
    const bool fade_out) {
  m_occurences = update_occurences(sequences, identities, fade_out);
  // convert occurences to probabilities
  for (auto& occ: m_occurences) {
    size_t i = 0;
    for (auto& v: occ.second) {
      occ.second[i] = v / sequences.size();
      ++i;
    }
  }
  // create an empty score map
  std::unordered_map<std::string, Scores> scores;
  for (auto& f: m_features) {
    scores[f] = std::vector<double>(sequences[0].residues.size(), 0);
  }
  for (size_t i = 0; i < sequences[0].residues.size(); ++i) {
    for (auto &feat : m_features){
      if (feat.substr(0, 2) == "p_") {
        scores[feat][i] = score_ptm(i, feat);
      } else if (feat.substr(0, 2) == "d_") {
        scores[feat][i] = score_domain(i, feat);
      } else if (feat.substr(0, 2) == "m_") {
        scores[feat][i] = score_motif(i, feat);
      } else if (feat.substr(0, 2) == "s_") {
        scores[feat][i] = score_strct(i, feat);
      }
      else if (feat.substr(0, 3) == "USR") {
        scores[feat][i] = score_usr_feature(i, feat, f_set.at(feat));
      }
    }
  }
  m_scores = scores;
}