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//
// 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
#include <utility>
#include "absl/status/statusor.h"
#include "absl/strings/string_view.h"
#include "alphafold3/parsers/cpp/fasta_iterator_lib.h"
#include "pybind11/attr.h"
#include "pybind11/pybind11.h"
#include "pybind11/pytypes.h"
#include "pybind11/stl.h"
namespace alphafold3 {
namespace {
namespace py = pybind11;
template <typename T>
T ValueOrThrowValueError(absl::StatusOr<T> value) {
if (!value.ok()) throw py::value_error(value.status().ToString());
return *std::move(value);
}
constexpr char kFastaFileIteratorDoc[] = R"(
Lazy FASTA parser for memory efficient FASTA parsing from a path.)";
constexpr char kFastaStringIteratorDoc[] = R"(
Lazy FASTA parser for memory efficient FASTA parsing from a string.
WARNING: The object backing the fasta_string string_view must not be
deleted while the FastaStringIterator is alive. E.g. this will break:
```
# Make sure the fasta_string is not interned.
fasta_string = '\n'.join(['>d\nS' for _ in range(10)])
iterator = fasta_iterator.FastaStringIterator(fasta_string)
del fasta_string
iterator.next() # Heap use-after-free.
```
)";
constexpr char kParseFastaDoc[] = R"(
Parses a FASTA string and returns a list of amino-acid sequences.
Args:
fasta_string: The contents of a FASTA file.
Returns:
List of sequences in the FASTA file. Descriptions are ignored.
)";
constexpr char kParseFastaIncludeDescriptionsDoc[] = R"(
Parses a FASTA string, returns amino-acid sequences with descriptions.
Args:
fasta_string: The contents of a FASTA file.
Returns:
A tuple with two lists (sequences, descriptions):
* A list of sequences.
* A list of sequence descriptions taken from the comment lines. In the
same order as the sequences.
)";
class PythonFastaStringIterator : public FastaStringIterator {
public:
explicit PythonFastaStringIterator(py::object fasta_string)
: FastaStringIterator(py::cast<absl::string_view>(fasta_string)),
fasta_string_(std::move(fasta_string)) {}
private:
py::object fasta_string_;
};
} // namespace
void RegisterModuleFastaIterator(pybind11::module m) {
py::class_<FastaFileIterator>(m, "FastaFileIterator", kFastaFileIteratorDoc)
.def(py::init<absl::string_view>(), py::arg("fasta_path"))
.def("__iter__",
[](FastaFileIterator& iterator) -> FastaFileIterator& {
return iterator;
})
.def(
"__next__",
[](FastaFileIterator& iterator) {
if (iterator.HasNext()) {
return ValueOrThrowValueError(iterator.Next());
} else {
throw py::stop_iteration();
}
},
py::call_guard<py::gil_scoped_release>());
py::class_<PythonFastaStringIterator>(m, "FastaStringIterator",
kFastaStringIteratorDoc)
.def(py::init<py::object>(), py::arg("fasta_string"))
.def("__iter__",
[](PythonFastaStringIterator& iterator)
-> PythonFastaStringIterator& { return iterator; })
.def(
"__next__",
[](PythonFastaStringIterator& iterator) {
if (iterator.HasNext()) {
return ValueOrThrowValueError(iterator.Next());
} else {
throw py::stop_iteration();
}
},
py::call_guard<py::gil_scoped_release>());
m.def("parse_fasta", &ParseFasta, py::arg("fasta_string"),
py::call_guard<py::gil_scoped_release>(), py::doc(kParseFastaDoc + 1));
m.def("parse_fasta_include_descriptions", &ParseFastaIncludeDescriptions,
py::arg("fasta_string"), py::call_guard<py::gil_scoped_release>(),
py::doc(kParseFastaIncludeDescriptionsDoc + 1));
}
} // namespace alphafold3
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