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* Copyright 2024 DeepMind Technologies Limited
*
* AlphaFold 3 source code is licensed under CC BY-NC-SA 4.0. To view a copy of
* this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/
*
* To request access to the AlphaFold 3 model parameters, follow the process set
* out at https://github.com/google-deepmind/alphafold3. You may only use these
* if received directly from Google. Use is subject to terms of use available at
* https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md
*/
// A C++ implementation of a FASTA parser.
#ifndef ALPHAFOLD3_SRC_ALPHAFOLD3_PARSERS_PYTHON_FASTA_ITERATOR_LIB_H_
#define ALPHAFOLD3_SRC_ALPHAFOLD3_PARSERS_PYTHON_FASTA_ITERATOR_LIB_H_
#include <fstream>
#include <ios>
#include <optional>
#include <string>
#include <utility>
#include <vector>
#include "absl/status/statusor.h"
#include "absl/strings/string_view.h"
namespace alphafold3 {
// Parse FASTA string and return list of strings with amino acid sequences.
// Returns a list of amino acid sequences only.
std::vector<std::string> ParseFasta(absl::string_view fasta_string);
// Parse FASTA string and return list of strings with amino acid sequences.
// Returns two lists: The first one with amino acid sequences, the second with
// the descriptions associated with each sequence.
std::pair<std::vector<std::string>, std::vector<std::string>>
ParseFastaIncludeDescriptions(absl::string_view fasta_string);
// Lazy FASTA parser for memory efficient FASTA parsing from a path.
class FastaFileIterator {
public:
// Initialise FastaFileIterator with filename of fasta. If you initialize
// reader_ with an invalid path or empty file, it won't fail, only
// riegeli::ReadLine within the Next method will then return false. That will
// then trigger the "Invalid FASTA file" error.
explicit FastaFileIterator(absl::string_view fasta_path)
: filename_(fasta_path),
reader_(filename_, std::ios::in),
has_next_(true) {}
// Returns whether there are more sequences. Returns true before first call to
// next even if the file is empty.
bool HasNext() const { return has_next_; }
// Fetches the next (sequence, description) from the file.
absl::StatusOr<std::pair<std::string, std::string>> Next();
private:
// Use riegeli::FileReader instead of FileLineIterator for about 2x speedup.
std::string filename_;
std::fstream reader_;
std::optional<std::string> description_;
std::string sequence_;
bool has_next_;
};
// Lazy FASTA parser for memory efficient FASTA parsing from a string.
class FastaStringIterator {
public:
// Initialise FastaStringIterator with a string_view of a FASTA. If you
// initialize it with an invalid FASTA string, it won't fail, the Next method
// will then return false. That will then trigger the "Invalid FASTA" error.
// WARNING: The object backing the fasta_string string_view must not be
// deleted while this Iterator is alive.
explicit FastaStringIterator(absl::string_view fasta_string)
: fasta_string_(fasta_string), has_next_(true) {}
// Returns whether there are more sequences. Returns true before first call to
// next even if the string is empty.
bool HasNext() const { return has_next_; }
// Fetches the next (sequence, description) from the string.
absl::StatusOr<std::pair<std::string, std::string>> Next();
private:
absl::string_view fasta_string_;
bool has_next_;
std::optional<std::string> description_;
std::string sequence_;
};
} // namespace alphafold3
#endif // ALPHAFOLD3_SRC_ALPHAFOLD3_PARSERS_PYTHON_FASTA_ITERATOR_LIB_H_
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