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