Module epiclass.core.data_source

Module for reading source data files.

Classes

class EpiDataSource (hdf5: Path, chromsize: Path, metadata: Path)

Used to contain source files.

Expand source code

class EpiDataSource:
    """Used to contain source files."""

    def __init__(self, hdf5: Path, chromsize: Path, metadata: Path):
        self._hdf5 = hdf5
        self._chromsize = chromsize
        self._metadata = metadata
        self.check_paths()

    @property
    def hdf5_file(self) -> Path:
        """Return hdf5 list file path."""
        return self._hdf5

    @property
    def chromsize_file(self) -> Path:
        """Return chromsize file path."""
        return self._chromsize

    @property
    def metadata_file(self) -> Path:
        """Return metadata file path."""
        return self._metadata

    def check_paths(self) -> None:
        """Make sure files exist. Raise error otherwise"""
        for path in [self._hdf5, self._chromsize, self._metadata]:
            if not path.is_file():
                raise OSError(
                    f"File does not exist : {path}.\n Expected file at : {path.resolve()}"
                )

    @staticmethod
    def get_file_list(hdf5_list_path: Path) -> List[Path]:
        """Return list of hdf5 files."""
        with open(hdf5_list_path, "r", encoding="utf-8") as my_file:
            return [Path(line.rstrip("\n")) for line in my_file]

    def hdf5_resolution(self) -> int:
        """Return resolution as an integer."""
        with open(self.hdf5_file, "r", encoding="utf-8") as my_file:
            first_path = Path(next(my_file).rstrip())
            try:
                resolution = self.get_file_hdf5_resolution(first_path)
            except (KeyError, FileNotFoundError) as err:
                warnings.warn(f"{err}. Seeking resolution from filename.")
                try:
                    resolution = self.get_resolution_from_filename(first_path)
                except KeyError as err2:
                    raise KeyError(
                        f"Filename does not contain resolution: {first_path}"
                    ) from err2
        return resolution

    @staticmethod
    def get_resolution_from_filename(path: Path) -> int:
        """Return resolution as an integer."""
        resolution_string = path.name.split("_")[1]
        return HDF5_RESOLUTION[resolution_string]

    @staticmethod
    def get_file_hdf5_resolution(hdf5_file: Path) -> int:
        """Return resolution as an integer."""
        with h5py.File(hdf5_file, "r") as h5_file:
            try:
                resolution = int(h5_file.attrs["bin"][0])  # type: ignore
            except KeyError as err:
                raise KeyError(
                    f"Resolution not found in {hdf5_file}. (attribute 'bin' does not exist)"
                ) from err
        return resolution

    @staticmethod
    def load_external_chrom_file(chrom_file: Path | str) -> List[Tuple[str, int]]:
        """Return sorted list with chromosome (name, size) pairs."""
        with open(chrom_file, "r", encoding="utf-8") as my_file:
            pairs = [line.rstrip("\n").split() for line in my_file]
        return sorted([(name, int(size)) for name, size in pairs])

    def load_chrom_sizes(self) -> List[Tuple[str, int]]:
        """Return sorted list with chromosome (name, size) pairs. This order
        is the same as the order of chroms in the concatenated signals.
        """
        return self.load_external_chrom_file(self.chromsize_file)

Static methods

def get_file_hdf5_resolution(hdf5_file: Path) ‑> int

Return resolution as an integer.

def get_file_list(hdf5_list_path: Path) ‑> List[pathlib.Path]

Return list of hdf5 files.

def get_resolution_from_filename(path: Path) ‑> int

Return resolution as an integer.

def load_external_chrom_file(chrom_file: Path | str)

Return sorted list with chromosome (name, size) pairs.

Instance variables

prop chromsize_file : Path

Return chromsize file path.

Expand source code

@property
def chromsize_file(self) -> Path:
    """Return chromsize file path."""
    return self._chromsize

prop hdf5_file : Path

Return hdf5 list file path.

Expand source code

@property
def hdf5_file(self) -> Path:
    """Return hdf5 list file path."""
    return self._hdf5

prop metadata_file : Path

Return metadata file path.

Expand source code

@property
def metadata_file(self) -> Path:
    """Return metadata file path."""
    return self._metadata

Methods

def check_paths(self) ‑> None

Make sure files exist. Raise error otherwise

def hdf5_resolution(self) ‑> int

Return resolution as an integer.

def load_chrom_sizes(self) ‑> List[Tuple[str, int]]

Return sorted list with chromosome (name, size) pairs. This order is the same as the order of chroms in the concatenated signals.