Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libctabix.pyi @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 import sys
2 from typing import Optional, List, Any
3
4 if sys.version_info < (3, 8):
5 from typing_extensions import Literal
6 else:
7 from typing import Literal
8
9 from pysam.libchtslib import HTSFile
10
11 _ParseResult = Any
12
13 class Parser:
14 def __init__(self, encoding: str = ...) -> None: ...
15 def get_encoding(self) -> str: ...
16 def set_encoding(self, encoding: str) -> None: ...
17 def __call__(self, buffer: str, length: int) -> _ParseResult: ...
18
19 class asTuple(Parser): ...
20 class asGFF3(Parser): ...
21 class asGTF(Parser): ...
22 class asBed(Parser): ...
23 class asVCF(Parser): ...
24
25 class TabixFile(HTSFile):
26 filename_index: bytes = ...
27 @property
28 def header(self) -> List[str]: ...
29 @property
30 def contigs(self) -> List[str]: ...
31 def __init__(
32 self,
33 filename: str,
34 mode: str = ...,
35 parser: Parser = ...,
36 index: Optional[str] = ...,
37 encoding: str = ...,
38 threads: int = ...,
39 *args,
40 **kwargs
41 ) -> None: ...
42 def fetch(
43 self,
44 reference: Optional[str] = ...,
45 start: Optional[int] = ...,
46 end: Optional[int] = ...,
47 region: Optional[str] = ...,
48 parser: Optional[Parser] = ...,
49 multiple_iterators: bool = ...,
50 ) -> Any: ...
51 def close(self) -> None: ...
52
53 class TabixIterator:
54 def __init__(self, encoding: str = ...) -> None: ...
55 def __iter__(self) -> TabixIterator: ...
56 def __next__(self) -> str: ...
57
58 class EmptyIterator:
59 def __iter__(self) -> Any: ...
60 def __next__(self) -> Any: ...
61
62 class TabixIteratorParsed(TabixIterator):
63 def __init__(self, parser: Parser) -> None: ...
64 def __next__(self) -> Any: ...
65
66 class GZIterator:
67 def __init__(
68 self, filename: str, bufer_size: int = ..., encoding: str = ...
69 ) -> None: ...
70 def __iter__(self) -> GZIterator: ...
71 def __next__(self) -> str: ...
72
73 class GZIteratorHead(GZIterator): ...
74
75 class GZIteratorParsed(GZIterator):
76 def __init__(self, parser: Parser) -> None: ...
77 def __next__(self) -> _ParseResult: ...
78
79 def tabix_compress(filename_in: str, filename_out: str, force: bool = ...) -> None: ...
80 def tabix_index(
81 filename: str,
82 force: bool = ...,
83 seq_col: Optional[int] = ...,
84 start_col: Optional[int] = ...,
85 end_col: Optional[int] = ...,
86 preset: Optional[Literal["gff", "bed", "sam", "vcf", "psltbl", "pileup"]] = ...,
87 meta_char: str = ...,
88 line_skip: int = ...,
89 zerobased: bool = ...,
90 min_shift: int = ...,
91 index: Optional[str] = ...,
92 keep_original: bool = ...,
93 csi: bool = ...,
94 ) -> str: ...
95
96 class tabix_file_iterator:
97 def __init__(self, infile: str, parser: Parser, buffer_size: int = ...) -> None: ...
98 def __iter__(self) -> tabix_file_iterator: ...
99 def __next__(self) -> _ParseResult: ...
100
101 class tabix_generic_iterator:
102 def __init__(self, infile: str, parser: Parser) -> None: ...
103 def __iter__(self) -> tabix_generic_iterator: ...
104 def __next__(self) -> _ParseResult: ...
105
106 def tabix_iterator(infile: str, parser: Optional[Parser]) -> _ParseResult: ...
107
108 # backwards compatibility
109 class Tabixfile(TabixFile): ...