Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcfaidx.pyi @ 68:5028fdace37b
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 16:23:26 -0400 |
| parents | |
| children |
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| 67:0e9998148a16 | 68:5028fdace37b |
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| 1 import array | |
| 2 from typing import Optional, Any, Sequence, Iterator | |
| 3 | |
| 4 class FastaFile: | |
| 5 def __init__( | |
| 6 self, | |
| 7 filename: str, | |
| 8 filepath_index: Optional[str] = ..., | |
| 9 filepath_index_compressed: Optional[str] = ..., | |
| 10 ) -> None: ... | |
| 11 def is_open(self) -> bool: ... | |
| 12 def __len__(self) -> int: ... | |
| 13 def close(self) -> None: ... | |
| 14 def __enter__(self) -> FastaFile: ... | |
| 15 def __exit__(self, type, value, traceback) -> Any: ... | |
| 16 @property | |
| 17 def closed(self) -> bool: ... | |
| 18 @property | |
| 19 def filename(self) -> str: ... | |
| 20 @property | |
| 21 def references(self) -> Sequence[str]: ... | |
| 22 @property | |
| 23 def nreferences(self) -> Optional[int]: ... | |
| 24 @property | |
| 25 def lengths(self) -> Sequence[int]: ... | |
| 26 def fetch( | |
| 27 self, | |
| 28 reference: Optional[str] = ..., | |
| 29 start: Optional[int] = ..., | |
| 30 end: Optional[int] = ..., | |
| 31 region: Optional[str] = ..., | |
| 32 ) -> str: ... | |
| 33 def get_reference_length(self, reference: str) -> int: ... | |
| 34 def __getitem__(self, reference: str) -> str: ... | |
| 35 def __contains__(self, reference: str) -> bool: ... | |
| 36 | |
| 37 | |
| 38 class FastqProxy: | |
| 39 @property | |
| 40 def name(self) -> str: ... | |
| 41 @property | |
| 42 def sequence(self) -> str: ... | |
| 43 @property | |
| 44 def comment(self) -> Optional[str]: ... | |
| 45 @property | |
| 46 def quality(self) -> Optional[str]: ... | |
| 47 def to_string(self) -> str: ... | |
| 48 def get_quality_array(self, offset: int = ...) -> Optional[array.array]: ... | |
| 49 | |
| 50 | |
| 51 class FastxRecord: | |
| 52 comment: Optional[str] = ... | |
| 53 quality: Optional[str] = ... | |
| 54 sequence: Optional[str] = ... | |
| 55 name: Optional[str] = ... | |
| 56 def __init__( | |
| 57 self, | |
| 58 name: Optional[str] = ..., | |
| 59 comment: Optional[str] = ..., | |
| 60 sequence: Optional[str] = ..., | |
| 61 quality: Optional[str] = ..., | |
| 62 ) -> None: ... | |
| 63 def set_name(self, name: str) -> None: ... | |
| 64 def set_comment(self, comment: str) -> None: ... | |
| 65 def set_sequence(self, sequence: str, quality: Optional[str] = ...) -> None: ... | |
| 66 def get_quality_array(self, offset: int = ...) -> array.array: ... | |
| 67 | |
| 68 class FastxFile: | |
| 69 def __init__(self, filename: str, persist: bool = ...) -> None: ... | |
| 70 def is_open(self) -> bool: ... | |
| 71 def close(self) -> None: ... | |
| 72 def __enter__(self) -> FastxFile: ... | |
| 73 def __exit__(self, type, value, traceback) -> Any: ... | |
| 74 @property | |
| 75 def closed(self) -> bool: ... | |
| 76 @property | |
| 77 def filename(self) -> str: ... | |
| 78 def __iter__(self) -> Iterator[FastxRecord]: ... | |
| 79 def __next__(self) -> FastxRecord: ... | |
| 80 | |
| 81 # deprecated | |
| 82 class FastqFile(FastxFile): ... |