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Refactor #5

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merged 5 commits into from
Aug 3, 2023
Merged

Refactor #5

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8a7cf81
Restructure project
robomics Aug 1, 2023
b66fd61
Refactor
robomics Aug 3, 2023
74603dc
Expose more properties of class Pixel*
robomics Aug 3, 2023
23b2f51
Add method to retrieve file attributes
robomics Aug 3, 2023
9c54a35
Add more tests
robomics Aug 3, 2023
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20 changes: 13 additions & 7 deletions src/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -7,16 +7,22 @@ find_package(
COMPONENTS Interpreter Development.Module
REQUIRED)

# For some reason linking to std::filesystem breaks cibw builds for Apple Silicon
# find_package(Filesystem REQUIRED)
# For some reason linking to std::filesystem breaks cibw builds for Apple Silicon find_package(Filesystem REQUIRED)

find_package(pybind11 CONFIG REQUIRED)

pybind11_add_module(hictkpy MODULE hictkpy.cpp)
pybind11_add_module(
hictkpy
MODULE
hictkpy.cpp
hictkpy_file.cpp
hictkpy_pixel_selector.cpp)

target_include_directories(hictkpy PRIVATE include)
target_link_libraries(
hictkpy
PRIVATE hictkpy_project_options hictkpy_project_warnings
PUBLIC hictk::cooler
hictk::file
hictk::hic)
PRIVATE hictkpy_project_options
hictkpy_project_warnings
hictk::cooler
hictk::file
hictk::hic)
187 changes: 88 additions & 99 deletions src/hictkpy.cpp
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Expand Up @@ -2,103 +2,95 @@
//
// SPDX-License-Identifier: MIT

#include <pybind11/operators.h>
#include <pybind11/pybind11.h>

#include "./common.hpp"
#include "./hictkpy_cooler.hpp"
#include "./hictkpy_file.hpp"
#include "./hictkpy_hic.hpp"
#include "hictk/cooler/cooler.hpp"
#include "hictk/file.hpp"
#include "hictk/hic.hpp"
#include "hictk/hic/utils.hpp"
#include "hictkpy/common.hpp"
#include "hictkpy/file.hpp"
#include "hictkpy/pixel_selector.hpp"

namespace py = pybind11;
namespace hictkpy {

static pybind11::module_ declare_cooler_submodule(pybind11::module_ &m) {
auto cooler = m.def_submodule("cooler");
auto cooler_utils = cooler.def_submodule("utils");

cooler_utils.def("is_cooler", &cooler::is_cooler, "test whether path points to a cooler file");

auto cooler_file =
py::class_<hictk::cooler::File>(cooler, "File")
.def(py::init(py::overload_cast<std::string_view>(cooler::file_ctor)), py::arg("uri"))
.def(py::init(py::overload_cast<std::string_view, const py::dict &, std::uint32_t, bool>(
cooler::file_ctor)),
py::arg("uri"), py::arg("chromosomes"), py::arg("bin_size"),
py::arg("overwrite_if_exists"));

cooler_file.def("uri", &hictk::cooler::File::uri);
cooler_file.def("hdf5_path", &hictk::cooler::File::hdf5_path);
cooler_file.def("path", &hictk::cooler::File::path);

cooler_file.def("bin_size", &hictk::cooler::File::bin_size);
cooler_file.def("nbins", &hictk::cooler::File::nbins);
cooler_file.def("nchroms", &hictk::cooler::File::nchroms);
cooler_file.def("nnz", &hictk::cooler::File::nnz);

cooler_file.def("chromosomes", &get_chromosomes_from_file<hictk::cooler::File>,
py::arg("include_all") = false);
cooler_file.def("bins", &get_bins_from_file<hictk::cooler::File>);
cooler_file.def("attributes", &cooler::get_cooler_attrs);

cooler_file.def("fetch", &cooler::fetch, py::arg("range1") = "", py::arg("range2") = "",
py::arg("normalization") = "NONE", py::arg("count_type") = "int",
py::arg("join") = false, py::arg("query_type") = "UCSC");
cooler_file.def("fetch_sparse", &cooler::fetch_sparse, py::arg("range1") = "",
py::arg("range2") = "", py::arg("normalization") = "NONE",
py::arg("count_type") = "int", py::arg("query_type") = "UCSC");
cooler_file.def("fetch_dense", &cooler::fetch_dense, py::arg("range1") = "",
py::arg("range2") = "", py::arg("normalization") = "NONE",
py::arg("count_type") = "int", py::arg("query_type") = "UCSC");
cooler_file.def("fetch_sum", &cooler::fetch_sum, py::arg("range1") = "", py::arg("range2") = "",
py::arg("normalization") = "NONE", py::arg("count_type") = "int",
py::arg("query_type") = "UCSC");
cooler_file.def("fetch_nnz", &cooler::fetch_nnz, py::arg("range1") = "", py::arg("range2") = "",
py::arg("query_type") = "UCSC");

return cooler;
template <typename N>
static void declare_thin_pixel_class(pybind11::module_ &m, const std::string &suffix) {
const auto type_name = std::string{"ThinPixel"} + suffix;
py::class_<hictk::ThinPixel<N>>(m, type_name.c_str())
.def_property_readonly("bin1_id", [](const hictk::ThinPixel<N> &tp) { return tp.bin1_id; })
.def_property_readonly("bin2_id", [](const hictk::ThinPixel<N> &tp) { return tp.bin2_id; })
.def_property_readonly("count", [](const hictk::ThinPixel<N> &tp) { return tp.count; })
.def("__repr__",
[](const hictk::ThinPixel<N> &tp) {
return fmt::format(FMT_COMPILE("bin1_id={}; bin2_id={}; count={};"), tp.bin1_id,
tp.bin2_id, tp.count);
})
.def("__str__", [](const hictk::ThinPixel<N> &tp) {
return fmt::format(FMT_COMPILE("{}\t{}\t{}"), tp.bin1_id, tp.bin2_id, tp.count);
});
}

template <typename N>
static void declare_pixel_class(pybind11::module_ &m, const std::string &suffix) {
const auto type_name = std::string{"Pixel"} + suffix;
py::class_<hictk::Pixel<N>>(m, type_name.c_str())
.def_property_readonly("bin1_id", [](const hictk::Pixel<N> &p) { return p.coords.bin1.id(); })
.def_property_readonly("bin2_id", [](const hictk::Pixel<N> &p) { return p.coords.bin2.id(); })
.def_property_readonly("rel_bin1_id",
[](const hictk::Pixel<N> &p) { return p.coords.bin1.rel_id(); })
.def_property_readonly("rel_bin2_id",
[](const hictk::Pixel<N> &p) { return p.coords.bin2.rel_id(); })
.def_property_readonly("chrom1",
[](const hictk::Pixel<N> &p) { return p.coords.bin1.chrom().name(); })
.def_property_readonly("start1",
[](const hictk::Pixel<N> &p) { return p.coords.bin1.start(); })
.def_property_readonly("end1", [](const hictk::Pixel<N> &p) { return p.coords.bin1.end(); })
.def_property_readonly("chrom2",
[](const hictk::Pixel<N> &p) { return p.coords.bin2.chrom().name(); })
.def_property_readonly("start2",
[](const hictk::Pixel<N> &p) { return p.coords.bin2.start(); })
.def_property_readonly("end2", [](const hictk::Pixel<N> &p) { return p.coords.bin2.end(); })
.def_property_readonly("count", [](const hictk::Pixel<N> &p) { return p.count; })
.def("__repr__",
[](const hictk::Pixel<N> &p) {
return fmt::format(
FMT_COMPILE("chrom1={}; start1={}; end1={}; chrom2={}; start2={}; end2={};"),
p.coords.bin1.chrom().name(), p.coords.bin1.start(), p.coords.bin1.end(),
p.coords.bin2.chrom().name(), p.coords.bin2.start(), p.coords.bin2.end(), p.count);
})
.def("__str__", [](const hictk::Pixel<N> &p) {
return fmt::format(FMT_COMPILE("{}\t{}\t{}\t{}\t{}\t{}"), p.coords.bin1.chrom().name(),
p.coords.bin1.start(), p.coords.bin1.end(), p.coords.bin2.chrom().name(),
p.coords.bin2.start(), p.coords.bin2.end(), p.count);
});
}

static pybind11::module_ declare_hic_submodule(pybind11::module_ &m) {
auto hic = m.def_submodule("hic");
auto hic_utils = hic.def_submodule("utils");

hic_utils.def("is_hic_file", &hictk::hic::utils::is_hic_file,
"test whether path points to a .hic file");

auto hic_file = py::class_<hictk::hic::File>(hic, "File")
.def(py::init(&hic::file_ctor), py::arg("path"), py::arg("resolution"),
py::arg("matrix_type") = "observed", py::arg("matrix_unit") = "BP");

hic_file.def("path", &hictk::hic::File::url);
hic_file.def("name", &hictk::hic::File::name);
hic_file.def("version", &hictk::hic::File::version);

hic_file.def("bin_size", &hictk::hic::File::resolution);
hic_file.def("nbins", &hictk::hic::File::nbins);
hic_file.def("nchroms", &hictk::hic::File::nchroms);

hic_file.def("chromosomes", &get_chromosomes_from_file<hictk::hic::File>,
py::arg("include_all") = false);
hic_file.def("bins", &get_bins_from_file<hictk::hic::File>);

hic_file.def("fetch", &hic::fetch, py::arg("range1") = "", py::arg("range2") = "",
py::arg("normalization") = "NONE", py::arg("count_type") = "int",
py::arg("join") = false, py::arg("query_type") = "UCSC");
hic_file.def("fetch_sparse", &hic::fetch_sparse, py::arg("range1") = "", py::arg("range2") = "",
py::arg("normalization") = "NONE", py::arg("count_type") = "int",
py::arg("query_type") = "UCSC");
hic_file.def("fetch_dense", &hic::fetch_dense, py::arg("range1") = "", py::arg("range2") = "",
py::arg("normalization") = "NONE", py::arg("count_type") = "int",
py::arg("query_type") = "UCSC");
hic_file.def("fetch_sum", &hic::fetch_sum, py::arg("range1") = "", py::arg("range2") = "",
py::arg("normalization") = "NONE", py::arg("count_type") = "int",
py::arg("query_type") = "UCSC");
hic_file.def("fetch_nnz", &hic::fetch_nnz, py::arg("range1") = "", py::arg("range2") = "",
py::arg("query_type") = "UCSC");
return hic;
static void declare_pixel_selector_class(pybind11::module_ &m) {
auto sel =
py::class_<PixelSelector>(m, "PixelSelector")
.def(py::init<std::shared_ptr<const hictk::cooler::PixelSelector>, std::string_view,
bool>(),
py::arg("selector"), py::arg("type"), py::arg("join"))
.def(py::init<std::shared_ptr<const hictk::hic::PixelSelector>, std::string_view, bool>(),
py::arg("selector"), py::arg("type"), py::arg("join"))
.def(py::init<std::shared_ptr<const hictk::hic::PixelSelectorAll>, std::string_view,
bool>(),
py::arg("selector"), py::arg("type"), py::arg("join"));

sel.def("coord1", &PixelSelector::get_coord1);
sel.def("coord2", &PixelSelector::get_coord2);

sel.def("__iter__", &PixelSelector::make_iterable, py::keep_alive<0, 1>());

sel.def("to_df", &PixelSelector::to_df);
sel.def("to_numpy", &PixelSelector::to_numpy);
sel.def("to_coo", &PixelSelector::to_coo);

sel.def("nnz", &PixelSelector::nnz);
sel.def("sum", &PixelSelector::sum);
}

static void declare_file_class(pybind11::module_ &m) {
Expand All @@ -119,20 +111,11 @@ static void declare_file_class(pybind11::module_ &m) {
file.def("nbins", &hictk::File::nbins);
file.def("nchroms", &hictk::File::nchroms);

file.def("attributes", &file::attributes);

file.def("fetch", &file::fetch, py::arg("range1") = "", py::arg("range2") = "",
py::arg("normalization") = "NONE", py::arg("count_type") = "int",
py::arg("join") = false, py::arg("query_type") = "UCSC");
file.def("fetch_sparse", &file::fetch_sparse, py::arg("range1") = "", py::arg("range2") = "",
py::arg("normalization") = "NONE", py::arg("count_type") = "int",
py::arg("query_type") = "UCSC");
file.def("fetch_dense", &file::fetch_dense, py::arg("range1") = "", py::arg("range2") = "",
py::arg("normalization") = "NONE", py::arg("count_type") = "int",
py::arg("query_type") = "UCSC");
file.def("fetch_sum", &file::fetch_sum, py::arg("range1") = "", py::arg("range2") = "",
py::arg("normalization") = "NONE", py::arg("count_type") = "int",
py::arg("query_type") = "UCSC");
file.def("fetch_nnz", &file::fetch_nnz, py::arg("range1") = "", py::arg("range2") = "",
py::arg("query_type") = "UCSC");
}

namespace py = pybind11;
Expand All @@ -146,9 +129,15 @@ PYBIND11_MODULE(hictkpy, m) {

m.doc() = "Blazing fast toolkit to work with .hic and .cool files";

declare_cooler_submodule(m);
declare_hic_submodule(m);
m.def("is_cooler", &file::is_cooler, "test whether path points to a cooler file");
m.def("is_hic_file", &hictk::hic::utils::is_hic_file, "test whether path points to a .hic file");

declare_file_class(m);
declare_pixel_selector_class(m);
declare_thin_pixel_class<std::int32_t>(m, "Int");
declare_thin_pixel_class<double>(m, "FP");
declare_pixel_class<std::int32_t>(m, "Int");
declare_pixel_class<double>(m, "FP");
}

} // namespace hictkpy
134 changes: 0 additions & 134 deletions src/hictkpy_cooler.hpp
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