jpayne@69: import array
jpayne@69: from typing import Optional, Any, Sequence, Iterator
jpayne@69: 
jpayne@69: class FastaFile:
jpayne@69:     def __init__(
jpayne@69:         self,
jpayne@69:         filename: str,
jpayne@69:         filepath_index: Optional[str] = ...,
jpayne@69:         filepath_index_compressed: Optional[str] = ...,
jpayne@69:     ) -> None: ...
jpayne@69:     def is_open(self) -> bool: ...
jpayne@69:     def __len__(self) -> int: ...
jpayne@69:     def close(self) -> None: ...
jpayne@69:     def __enter__(self) -> FastaFile: ...
jpayne@69:     def __exit__(self, type, value, traceback) -> Any: ...
jpayne@69:     @property
jpayne@69:     def closed(self) -> bool: ...
jpayne@69:     @property
jpayne@69:     def filename(self) -> str: ...
jpayne@69:     @property
jpayne@69:     def references(self) -> Sequence[str]: ...
jpayne@69:     @property
jpayne@69:     def nreferences(self) -> Optional[int]: ...
jpayne@69:     @property
jpayne@69:     def lengths(self) -> Sequence[int]: ...
jpayne@69:     def fetch(
jpayne@69:         self,
jpayne@69:         reference: Optional[str] = ...,
jpayne@69:         start: Optional[int] = ...,
jpayne@69:         end: Optional[int] = ...,
jpayne@69:         region: Optional[str] = ...,
jpayne@69:     ) -> str: ...
jpayne@69:     def get_reference_length(self, reference: str) -> int: ...
jpayne@69:     def __getitem__(self, reference: str) -> str: ...
jpayne@69:     def __contains__(self, reference: str) -> bool: ...
jpayne@69: 
jpayne@69:         
jpayne@69: class FastqProxy:
jpayne@69:     @property
jpayne@69:     def name(self) -> str: ...
jpayne@69:     @property
jpayne@69:     def sequence(self) -> str: ...
jpayne@69:     @property
jpayne@69:     def comment(self) -> Optional[str]: ...
jpayne@69:     @property
jpayne@69:     def quality(self) -> Optional[str]: ...
jpayne@69:     def to_string(self) -> str: ...
jpayne@69:     def get_quality_array(self, offset: int = ...) -> Optional[array.array]: ...
jpayne@69:     
jpayne@69:         
jpayne@69: class FastxRecord:
jpayne@69:     comment: Optional[str] = ...
jpayne@69:     quality: Optional[str] = ...
jpayne@69:     sequence: Optional[str] = ...
jpayne@69:     name: Optional[str] = ...
jpayne@69:     def __init__(
jpayne@69:         self,
jpayne@69:         name: Optional[str] = ...,
jpayne@69:         comment: Optional[str] = ...,
jpayne@69:         sequence: Optional[str] = ...,
jpayne@69:         quality: Optional[str] = ...,
jpayne@69:     ) -> None: ...
jpayne@69:     def set_name(self, name: str) -> None: ...
jpayne@69:     def set_comment(self, comment: str) -> None: ...
jpayne@69:     def set_sequence(self, sequence: str, quality: Optional[str] = ...) -> None: ...
jpayne@69:     def get_quality_array(self, offset: int = ...) -> array.array: ...
jpayne@69: 
jpayne@69: class FastxFile:
jpayne@69:     def __init__(self, filename: str, persist: bool = ...) -> None: ...
jpayne@69:     def is_open(self) -> bool: ...
jpayne@69:     def close(self) -> None: ...
jpayne@69:     def __enter__(self) -> FastxFile: ...
jpayne@69:     def __exit__(self, type, value, traceback) -> Any: ...
jpayne@69:     @property
jpayne@69:     def closed(self) -> bool: ...
jpayne@69:     @property
jpayne@69:     def filename(self) -> str: ...
jpayne@69:     def __iter__(self) -> Iterator[FastxRecord]: ...
jpayne@69:     def __next__(self) -> FastxRecord: ...
jpayne@69: 
jpayne@69: # deprecated
jpayne@69: class FastqFile(FastxFile): ...