Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pysam/libcalignmentfile.pyi @ 68:5028fdace37b

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
parents
children
comparison
equal deleted inserted replaced
67:0e9998148a16 68:5028fdace37b
1 import array
2 import sys
3 from typing import (
4 Any,
5 Dict,
6 Type,
7 NamedTuple,
8 Tuple,
9 Optional,
10 Sequence,
11 Union,
12 Callable,
13 List,
14 Iterable,
15 )
16
17 if sys.version_info < (3, 8):
18 from typing_extensions import Literal
19 else:
20 from typing import Literal
21
22 from pysam.libchtslib import HTSFile, _HasFileNo
23 from pysam.libcalignedsegment import AlignedSegment, PileupColumn
24 from pysam.libcfaidx import FastaFile
25
26 class IndexStats(NamedTuple):
27 contig: str
28 mapped: int
29 unmapped: int
30 total: int
31
32 VALID_HEADER_TYPES: Dict[str, Type]
33 VALID_HEADERS: Tuple[str]
34 KNOWN_HEADER_FIELDS: Dict[str, Dict[str, Type]]
35 VALID_HEADER_ORDER: Dict[str, Tuple[str]]
36
37 def build_header_line(fields: Dict[str, str], record: str) -> str: ...
38
39 class AlignmentHeader:
40 def __init__(self) -> None: ...
41 @classmethod
42 def _from_text_and_lengths(
43 cls,
44 text: Optional[str],
45 reference_names: Optional[Sequence[str]],
46 reference_lengths: Optional[Sequence[int]],
47 ) -> AlignmentHeader: ...
48 @classmethod
49 def from_text(cls, text: str) -> AlignmentHeader: ...
50 @classmethod
51 def from_dict(cls, header_dict: Dict) -> AlignmentHeader: ...
52 @classmethod
53 def from_references(
54 cls,
55 reference_names: Sequence[str],
56 reference_lengths: Sequence[int],
57 text: Optional[str] = ...,
58 add_sq_text: bool = ...,
59 ) -> AlignmentHeader: ...
60 def __bool__(self) -> bool: ...
61 def copy(self) -> AlignmentHeader: ...
62 @property
63 def nreferences(self) -> int: ...
64 @property
65 def references(self) -> Tuple[str]: ...
66 @property
67 def lengths(self) -> Tuple[int]: ...
68 def to_dict(self) -> Dict: ...
69 def get_reference_name(self, tid: int) -> Optional[str]: ...
70 def get_reference_length(self, reference: str) -> int: ...
71 def is_valid_tid(self, tid: int) -> bool: ...
72 def get_tid(self, reference: str) -> int: ...
73
74 # The iterator produced by AlignmentFile is currently itself, but this may
75 # change in future and code should not make assumptions about this type.
76 AlignmentFileIterator = AlignmentFile
77
78 class AlignmentFile(HTSFile):
79 def __init__(
80 self,
81 filename: Union[str, bytes, int, _HasFileNo],
82 mode: Optional[
83 Literal["r", "w", "wh", "rb", "wb", "wbu", "wb0", "rc", "wc"]
84 ] = ...,
85 template: Optional[AlignmentFile] = ...,
86 reference_names: Optional[Sequence[str]] = ...,
87 reference_lengths: Optional[Sequence[int]] = ...,
88 reference_filename: Optional[str] = ...,
89 text: Optional[str] = ...,
90 header: Union[None, Dict, AlignmentHeader] = ...,
91 add_sq_text: bool = ...,
92 add_sam_header: bool = ...,
93 check_sq: bool = ...,
94 index_filename: Optional[str] = ...,
95 filepath_index: Optional[str] = ...,
96 require_index: bool = ...,
97 duplicate_filehandle: bool = ...,
98 ignore_truncation: bool = ...,
99 format_options: Optional[Sequence[str]] = ...,
100 threads: int = ...,
101 ) -> None: ...
102 def has_index(self) -> bool: ...
103 def check_index(self) -> bool: ...
104 def fetch(
105 self,
106 contig: Optional[str] = ...,
107 start: Optional[int] = ...,
108 stop: Optional[int] = ...,
109 region: Optional[str] = ...,
110 tid: Optional[int] = ...,
111 until_eof: bool = ...,
112 multiple_iterators: bool = ...,
113 reference: Optional[str] = ...,
114 end: int = ...,
115 ) -> IteratorRow: ...
116 def head(self, n: int, multiple_iterators: bool = ...) -> IteratorRow: ...
117 def mate(self, read: AlignedSegment) -> AlignedSegment: ...
118 def pileup(
119 self,
120 contig: Optional[str] = ...,
121 start: Optional[int] = ...,
122 stop: Optional[int] = ...,
123 region: Optional[str] = ...,
124 reference: Optional[str] = ...,
125 end: Optional[int] = ...,
126 truncate: bool = ...,
127 max_depth: int = ...,
128 stepper: str = ...,
129 fastafile: Optional[FastaFile] = ...,
130 ignore_overlaps: bool = ...,
131 flag_filter: int = ...,
132 flag_require: int = ...,
133 ignore_orphans: bool = ...,
134 min_base_quality: int = ...,
135 adjust_capq_threshold: int = ...,
136 min_mapping_quality: int = ...,
137 compute_baq: bool = ...,
138 redo_baq: bool = ...,
139 ) -> IteratorColumn: ...
140 def count(
141 self,
142 contig: Optional[str] = ...,
143 start: Optional[int] = ...,
144 stop: Optional[int] = ...,
145 region: Optional[str] = ...,
146 until_eof: bool = ...,
147 read_callback: Union[str, Callable[[AlignedSegment], bool]] = ...,
148 reference: Optional[str] = ...,
149 end: Optional[int] = ...,
150 ) -> int: ...
151 def count_coverage(
152 self,
153 contig: Optional[str] = ...,
154 start: Optional[int] = ...,
155 stop: Optional[int] = ...,
156 region: Optional[str] = ...,
157 quality_threshold: int = ...,
158 read_callback: Union[str, Callable[[AlignedSegment], bool]] = ...,
159 reference: Optional[str] = ...,
160 end: Optional[int] = ...,
161 ) -> Tuple[array.array, array.array, array.array, array.array]: ...
162 def find_introns_slow(
163 self, read_iterator: Iterable[AlignedSegment]
164 ) -> Dict[Tuple[int, int], int]: ...
165 def find_introns(
166 self, read_iterator: Iterable[AlignedSegment]
167 ) -> Dict[Tuple[int, int], int]: ...
168 def close(self) -> None: ...
169 def write(self, read: AlignedSegment) -> int: ...
170 def __enter__(self) -> AlignmentFile: ...
171 def __exit__(self, exc_type, exc_value, traceback): ...
172 @property
173 def mapped(self) -> int: ...
174 @property
175 def unmapped(self) -> int: ...
176 @property
177 def nocoordinate(self) -> int: ...
178 def get_index_statistics(self) -> List[IndexStats]: ...
179 def __iter__(self) -> AlignmentFileIterator: ...
180 def __next__(self) -> AlignedSegment: ...
181 def is_valid_tid(self, tid: int) -> bool: ...
182 def get_tid(self, reference: str) -> int: ...
183 def get_reference_name(self, tid: int) -> str: ...
184 def get_reference_length(self, reference: str) -> int: ...
185 @property
186 def nreferences(self) -> int: ...
187 @property
188 def references(self) -> Tuple[str, ...]: ...
189 @property
190 def lengths(self) -> Tuple[int, ...]: ...
191 @property
192 def reference_filename(self) -> Optional[str]: ...
193 @property
194 def header(self) -> AlignmentHeader: ...
195
196 class IteratorRow:
197 def __iter__(self) -> IteratorRow: ...
198 def __next__(self) -> AlignedSegment: ...
199
200 class IteratorRowAll(IteratorRow): ...
201 class IteratorRowAllRefs(IteratorRow): ...
202 class IteratorRowHead(IteratorRow): ...
203 class IteratorRowRegion(IteratorRow): ...
204 class IteratorRowSelection(IteratorRow): ...
205
206 class IteratorColumn:
207 def __iter__(self) -> IteratorColumn: ...
208 def __next__(self) -> PileupColumn: ...
209 @property
210 def seq_len(self) -> int: ...
211 def add_reference(self, fastafile: FastaFile) -> None: ...
212 def has_reference(self) -> bool: ...
213
214 class IteratorColumnAll(IteratorColumn): ...
215 class IteratorColumnAllRefs(IteratorColumn): ...
216 class IteratorColumnRegion(IteratorColumn): ...
217
218 class SNPCall:
219 @property
220 def tid(self) -> int: ...
221 @property
222 def pos(self) -> int: ...
223 @property
224 def reference_base(self) -> str: ...
225 @property
226 def genotype(self) -> str: ...
227 @property
228 def consensus_quality(self) -> int: ...
229 @property
230 def snp_quality(self) -> int: ...
231 @property
232 def mapping_quality(self) -> int: ...
233 @property
234 def coverage(self) -> int: ...
235
236 class IndexedReads:
237 def __init__(
238 self, samfile: AlignmentFile, multiple_iterators: bool = ...
239 ) -> None: ...
240 def build(self) -> None: ...
241 def find(self, query_name: str) -> IteratorRow: ...