Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcbcf.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 (
3 Optional,
4 Union,
5 Any,
6 Sequence,
7 Tuple,
8 Iterator,
9 List,
10 Iterable,
11 Dict,
12 overload,
13 TypeVar,
14 Mapping,
15 Generic,
16 )
17
18 if sys.version_info < (3, 8):
19 from typing_extensions import Literal
20 else:
21 from typing import Literal
22
23 from pysam.libchtslib import HTSFile, _HasFileNo
24
25 _D = TypeVar("_D")
26 _K = TypeVar("_K", str, Union[int, str])
27 _V = TypeVar("_V")
28
29 class _Mapping(Generic[_K, _V]):
30 def __len__(self) -> int: ...
31 def __contains__(self, key: _K) -> bool: ...
32 def __iter__(self) -> Iterator[_K]: ...
33 def iterkeys(self) -> Iterator[_K]: ...
34 def itervalues(self) -> Iterator[_V]: ...
35 def iteritems(self) -> Iterator[Tuple[_K, _V]]: ...
36 def keys(self) -> List[_K]: ...
37 def items(self) -> List[Tuple[_K, _V]]: ...
38 def values(self) -> List[_V]: ...
39 def __bool__(self) -> bool: ...
40 def __getitem__(self, key: _K) -> _V: ...
41 def get(self, key: _K, default: _D = ...) -> Union[_D, _V]: ...
42
43 class VariantHeaderRecord(_Mapping[str, str]):
44 @property
45 def header(self) -> VariantHeader: ...
46 @property
47 def type(self) -> Optional[str]: ...
48 @property
49 def key(self) -> Optional[str]: ...
50 @property
51 def value(self) -> Optional[str]: ...
52 @property
53 def attrs(self) -> Sequence[Tuple[str, str]]: ...
54 def update(self, items: Union[Iterable, Dict] = ..., **kwargs) -> None: ...
55 def pop(self, key: str, default: str = ...) -> str: ...
56 def remove(self) -> None: ... # crashes
57
58 class VariantHeaderRecords:
59 @property
60 def header(self) -> VariantHeader: ...
61 def __len__(self) -> int: ...
62 def __bool__(self) -> bool: ...
63 def __getitem__(self, index) -> VariantHeaderRecord: ...
64 def __iter__(self) -> Iterator[VariantHeaderRecord]: ...
65
66 class VariantMetadata:
67 @property
68 def header(self) -> VariantHeader: ...
69 @property
70 def name(self) -> str: ...
71 # @property # should this be exposed?
72 # def id(self) -> int: ...
73 @property
74 def number(self) -> Optional[str]: ...
75 @property
76 def type(self) -> Optional[str]: ...
77 @property
78 def description(self) -> Optional[str]: ...
79 @property
80 def record(self) -> Optional[VariantHeaderRecord]: ...
81 def remove_header(self) -> None: ...
82
83 class VariantHeaderMetadata(_Mapping[str, VariantMetadata]):
84 @property
85 def header(self) -> VariantHeader: ...
86 def add(
87 self,
88 id: str,
89 number: Optional[Union[int, str]],
90 type: Optional[str],
91 description: str,
92 **kwargs
93 ) -> None: ...
94 def remove_header(self, key: str) -> None: ...
95 def clear_header(self) -> None: ...
96
97 class VariantContig:
98 @property
99 def header(self) -> VariantHeader: ...
100 @property
101 def name(self) -> str: ...
102 @property
103 def id(self) -> int: ...
104 @property
105 def length(self) -> Optional[int]: ...
106 @property
107 def header_record(self) -> VariantHeaderRecord: ...
108 def remove_header(self) -> None: ...
109
110 class VariantHeaderContigs(_Mapping[Union[int, str], VariantContig]):
111 @property
112 def header(self) -> VariantHeader: ...
113 def remove_header(self, key: Union[int, str]) -> None: ...
114 def clear_header(self) -> None: ...
115 def add(self, id: str, length: Optional[int] = ..., **kwargs) -> None: ...
116
117 class VariantHeaderSamples:
118 @property
119 def header(self) -> VariantHeader: ...
120 def __len__(self) -> int: ...
121 def __bool__(self) -> bool: ...
122 def __getitem__(self, index: int) -> str: ...
123 def __iter__(self) -> Iterator[str]: ...
124 def __contains__(self, key: str) -> bool: ...
125 def add(self, name: str) -> None: ...
126
127 class VariantHeader:
128 def __init__(self) -> None: ...
129 def __bool__(self) -> bool: ...
130 def copy(self) -> VariantHeader: ...
131 def merge(self, header: VariantHeader) -> None: ...
132 @property
133 def version(self) -> str: ...
134 @property
135 def samples(self) -> VariantHeaderSamples: ...
136 @property
137 def records(self) -> VariantHeaderRecords: ...
138 @property
139 def contigs(self) -> VariantHeaderContigs: ...
140 @property
141 def filters(self) -> VariantHeaderMetadata: ...
142 @property
143 def info(self) -> VariantHeaderMetadata: ...
144 @property
145 def formats(self) -> VariantHeaderMetadata: ...
146 @property
147 def alts(self) -> Dict[str, VariantHeaderRecord]: ...
148 def new_record(
149 self,
150 contig: Optional[str] = ...,
151 start: int = ...,
152 stop: int = ...,
153 alleles: Optional[Tuple[str, ...]] = ...,
154 id: Optional[str] = ...,
155 qual: Optional[float] = ...,
156 filter: Optional[Any] = ...,
157 info: Optional[Mapping[str, _InfoValue]] = ...,
158 samples: Optional[Iterable[Optional[Mapping[str, _FormatValue]]]] = ...,
159 **kwargs
160 ) -> VariantRecord: ...
161 def add_record(self, record: VariantHeaderRecord) -> None: ...
162 def add_line(self, line: str) -> None: ...
163 @overload
164 def add_meta(
165 self, key: str, value: None = ..., items: Iterable[Tuple[str, str]] = ...
166 ) -> None: ...
167 @overload
168 def add_meta(self, key: str, value: str = ..., items: None = ...) -> None: ...
169 def add_sample(self, name: str) -> None: ...
170 def add_samples(self, *args: Union[str, Iterable[str]]) -> None: ...
171
172 class VariantRecordFilter(_Mapping[Union[int, str], VariantMetadata]):
173 def add(self, key: str) -> None: ...
174 def __delitem__(self, key: Union[int, str]) -> None: ...
175 def clear(self) -> None: ...
176 def __eq__(self, other) -> bool: ...
177 def __ne__(self, other) -> bool: ...
178
179 class VariantRecordFormat(_Mapping[str, VariantMetadata]):
180 def __delitem__(self, key: str) -> None: ...
181 def clear(self) -> None: ...
182
183 _InfoValue = Any # TODO see bcf_info_get_value
184
185 class VariantRecordInfo(_Mapping[str, _InfoValue]):
186 def __setitem__(self, key: str, object: _InfoValue) -> None: ...
187 def __delitem__(self, key: str) -> None: ...
188 def clear(self) -> None: ...
189 def update(
190 self, items: Optional[_Mapping[str, _InfoValue]] = ..., **kwargs
191 ) -> None: ...
192 def pop(self, key: str, default: _D = ...) -> Union[_D, _InfoValue]: ...
193 def __eq__(self, other) -> bool: ...
194 def __ne__(self, other) -> bool: ...
195
196 class VariantRecordSamples(_Mapping[Union[str, int], "VariantRecordSample"]):
197 def __eq__(self, other) -> bool: ...
198 def __ne__(self, other) -> bool: ...
199 # TODO Do these work? Isn’t the container read only?
200 def update(
201 self,
202 items: Optional[Mapping[Union[str, int], VariantRecordSample]] = ...,
203 **kwargs
204 ) -> None: ...
205 def pop(
206 self, key: Union[str, int], default: _D = ...
207 ) -> Union[_D, VariantRecordSample]: ...
208
209 class VariantRecord:
210 @property
211 def header(self) -> VariantHeader: ...
212 def copy(self) -> VariantRecord: ...
213 def translate(self, dst_header: VariantHeader) -> None: ...
214 rid: int
215 chrom: str
216 contig: str
217 pos: int
218 start: int
219 stop: int
220 rlen: int
221 qual: Optional[float]
222 id: Optional[str]
223 ref: Optional[str]
224 alleles: Optional[Tuple[str, ...]]
225 alts: Optional[Tuple[str, ...]]
226 @property
227 def filter(self) -> VariantRecordFilter: ...
228 @property
229 def info(self) -> VariantRecordInfo: ...
230 @property
231 def format(self) -> VariantRecordFormat: ...
232 @property
233 def samples(self) -> VariantRecordSamples: ...
234 def __eq__(self, other) -> bool: ...
235 def __ne__(self, other) -> bool: ...
236
237 _FormatValue = Any # TODO see bcf_format_get_value
238
239 class VariantRecordSample(_Mapping[str, _FormatValue]):
240 @property
241 def index(self) -> int: ...
242 @property
243 def name(self) -> str: ...
244 allele_indices: Optional[Tuple[Optional[int], ...]]
245 alleles: Optional[Tuple[Optional[str], ...]]
246 phased: bool
247 def __setitem__(self, key: str, value: _FormatValue) -> None: ...
248 def __delitem__(self, key: str) -> None: ...
249 def clear(self) -> None: ...
250 def update(
251 self, items: Optional[Mapping[str, _FormatValue]] = ..., **kwargs
252 ) -> None: ...
253 def pop(self, key: str, default: _D = ...) -> Union[_D, _FormatValue]: ...
254 def __eq__(self, other) -> Any: ...
255 def __ne__(self, other) -> Any: ...
256
257 class BaseIndex(_Mapping[Union[int, str], str]):
258 refs: Sequence[str]
259 refmap: Dict[str, str]
260 def __init__(self) -> None: ...
261 # TODO Do these work? Isn’t the container read only?
262 def update(self, items: Optional[Mapping[str, str]] = ..., **kwargs) -> None: ...
263 def pop(self, key: str, default: _D = ...) -> Union[_D, str]: ...
264
265 class BCFIndex(BaseIndex):
266 @property
267 def header(self) -> VariantHeader: ...
268 def __init__(self) -> None: ...
269 def fetch(
270 self,
271 bcf: VariantFile,
272 contig: str,
273 start: Optional[int],
274 stop: Optional[int],
275 reopen: bool,
276 ) -> BCFIterator: ...
277
278 class TabixIndex(BaseIndex):
279 def __init__(self) -> None: ...
280 def fetch(
281 self,
282 bcf: VariantFile,
283 contig: str,
284 start: Optional[int],
285 stop: Optional[int],
286 reopen: bool,
287 ) -> TabixIterator: ...
288
289 class BaseIterator:
290 def __init__(self) -> None: ...
291
292 class BCFIterator(BaseIterator):
293 def __init__(
294 self,
295 bcf: VariantFile,
296 contig: str,
297 start: Optional[int] = ...,
298 stop: Optional[int] = ...,
299 reopen: bool = ...,
300 ) -> None: ...
301 def __iter__(self) -> BCFIterator: ...
302 def __next__(self) -> VariantRecord: ...
303
304 class TabixIterator(BaseIterator):
305 def __init__(
306 self,
307 bcf: VariantFile,
308 contig: str,
309 start: Optional[int] = ...,
310 stop: Optional[int] = ...,
311 reopen: bool = ...,
312 ) -> None: ...
313 def __iter__(self) -> TabixIterator: ...
314 def __next__(self) -> VariantRecord: ...
315
316 class VariantFile(HTSFile):
317 @property
318 def header(self) -> VariantHeader: ...
319 @property
320 def index(self) -> BaseIndex: ...
321 @property
322 def drop_samples(self) -> bool: ...
323 @property
324 def is_reading(self) -> bool: ...
325 @property
326 def header_written(self) -> bool: ...
327 def __init__(
328 self,
329 filename: Union[str, bytes, int, _HasFileNo],
330 mode: Optional[Literal["r", "w", "wh", "rb", "wb", "wbu", "wb0"]] = ...,
331 index_filename: Optional[str] = ...,
332 header: Optional[VariantHeader] = ...,
333 drop_samples: bool = ...,
334 duplicate_filehandle: bool = ...,
335 ignore_truncation: bool = ...,
336 threads: int = ...,
337 ) -> None: ...
338 def close(self) -> None: ...
339 def __iter__(self) -> VariantFile: ...
340 def __next__(self) -> VariantRecord: ...
341 def copy(self) -> VariantFile: ...
342 def open(
343 self,
344 filename: Union[str, bytes, int, _HasFileNo],
345 mode: Optional[Literal["r", "w", "wh", "rb", "wb", "wbu", "wb0"]] = ...,
346 index_filename: Optional[str] = ...,
347 header: Optional[VariantHeader] = ...,
348 drop_samples: bool = ...,
349 duplicate_filehandle: bool = ...,
350 ignore_truncation: bool = ...,
351 threads: int = ...,
352 ) -> None: ...
353 def reset(self) -> None: ...
354 def is_valid_tid(self, tid: int) -> bool: ...
355 def get_tid(self, reference: str) -> int: ...
356 def get_reference_name(self, tid: int) -> str: ...
357 def fetch(
358 self,
359 contig: Optional[str] = ...,
360 start: Optional[int] = ...,
361 stop: Optional[int] = ...,
362 region: Optional[str] = ...,
363 reopen: bool = ...,
364 end: Optional[int] = ...,
365 reference: Optional[str] = ...,
366 ) -> Iterator[VariantRecord]: ...
367 def new_record(self, *args, **kwargs) -> Any: ...
368 def write(self, record: VariantRecord) -> int: ...
369 def subset_samples(self, include_samples: Iterable[str]) -> None: ...