pyaragorn 0.3.0__cp38-cp38-win_amd64.whl

pyaragorn/CMakeLists.txt

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+cython_extension(lib LINKS aragorn)

pyaragorn/__init__.py

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+from . import lib
+from .lib import (
+    __version__,
+    Gene,
+    TRNAGene,
+    TMRNAGene,
+    RNAFinder,
+    ARAGORN_VERSION,
+    TRANSLATION_TABLES,
+)
+
+__doc__ = lib.__doc__
+__all__ = [
+    "Gene",
+    "TRNAGene",
+    "TMRNAGene",
+    "RNAFinder",
+    "ARAGORN_VERSION",
+    "TRANSLATION_TABLES",
+]
+
+__author__ = "Martin Larralde <martin.larralde@embl.de>"
+__license__ = "GPL-3.0-or-later"
+
+# Small addition to the docstring: we want to show a link redirecting to the
+# rendered version of the documentation, but this can only work when Python
+# is running with docstrings enabled
+if __doc__ is not None:
+    __doc__ += """See Also:
+    An online rendered version of the documentation for this version
+    of the library on
+    `Read The Docs <https://pyaragorn.readthedocs.io/en/v{}/>`_.
+
+    """.format(
+        __version__
+    )

pyaragorn/lib.pyi

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+import typing
+from typing import Literal, Union, Generic
+from typing_extensions import Buffer
+
+__version__: str
+
+ARAGORN_VERSION: str
+TRANSLATION_TABLES: typing.Set[int]
+
+class Gene:
+    @property
+    def type(self) -> str: ...
+    @property
+    def begin(self) -> int: ...
+    @property
+    def end(self) -> int: ...
+    @property
+    def length(self) -> int: ...
+    @property
+    def strand(self) -> Literal[1, -1]: ...
+    @property
+    def energy(self) -> float: ...
+    @property
+    def raw_energy(self) -> float: ...
+    def sequence(self) -> str: ...
+ 
+class TRNAGene(Gene):
+    @property
+    def type(self) -> Literal["tRNA"]: ...
+    @property
+    def amino_acid(self) -> str: ...
+    @property
+    def amino_acids(self) -> Union[Tuple[str], Tuple[str, str]]: ...
+    @property
+    def anticodon(self) -> str: ...
+    @property
+    def anticodon_offset(self) -> int: ...
+    @property
+    def anticodon_length(self) -> Literal[2, 3, 4]: ...
+
+class TMRNAGene(Gene):
+    @property
+    def type(self) -> Literal["tmRNA"]: ...
+    @property
+    def permuted(self) -> bool: ...
+    @property
+    def orf_offset(self) -> int: ...
+    @property
+    def orf_length(self) -> int: ...
+    def orf(self, include_stop: bool = True) -> str: ...
+    def peptide(self, include_stop: bool = True) -> str: ...
+
+
+class Cursor:
+    def __init__(self, obj: Union[str, bytes, bytearray, Buffer]) -> None: ...
+
+
+G = typing.TypeVar("G", bound=Gene)
+
+class RNAFinder(Generic[G]):
+    @typing.overload
+    def __init__(
+        self: RNAFinder[TRNAGene],
+        translation_table: int = 1,
+        *,
+        tmrna: Literal[False],
+        trna: Literal[True] = True,
+        linear: bool = False,
+        threshold_scale: float = 1.0,
+    ) -> None: ...
+    @typing.overload
+    def __init__(
+        self: RNAFinder[TMRNAGene],
+        translation_table: int = 1,
+        *,
+        trna: Literal[False],
+        tmrna: Literal[True] = True,
+        linear: bool = False,
+        threshold_scale: float = 1.0,
+    ) -> None: ...
+    @typing.overload
+    def __init__(
+        self: RNAFinder[Union[TRNAGene, TMRNAGene]],
+        translation_table: int = 1,
+        *,
+        trna: bool = True,
+        tmrna: bool = True,
+        linear: bool = False,
+        threshold_scale: float = 1.0,
+    ) -> None: ...
+    def __repr__(self) -> str: ...
+    @property
+    def translation_table(self) -> int: ...
+    @property
+    def trna(self) -> bool: ...
+    @property
+    def tmrna(self) -> bool: ...
+    @property
+    def linear(self) -> bool: ...
+    @property
+    def threshold_scale(self) -> float: ...
+    @threshold_scale.setter
+    def threshold_scale(self, threshold_scale: float) -> None: ...
+    def find_rna(
+        self,
+        sequence: Union[str, bytes, bytearray, Buffer],
+    ) -> List[G]: ...