Coverage for phytest/bio/alignment.py : 100.00%
Hot-keys on this page
r m x p toggle line displays
j k next/prev highlighted chunk
0 (zero) top of page
1 (one) first highlighted chunk
1from typing import Optional
2from warnings import warn
4from Bio import AlignIO
5from Bio.Align import MultipleSeqAlignment
7from ..utils import PhytestObject, assert_or_warn
10class Alignment(PhytestObject, MultipleSeqAlignment):
11 @classmethod
12 def read(cls, alignment_path, alignment_format) -> 'Alignment':
13 alignment = AlignIO.read(alignment_path, alignment_format)
14 return Alignment(
15 alignment._records, annotations=alignment.annotations, column_annotations=alignment.column_annotations
16 )
18 def assert_width(
19 self,
20 width: Optional[int] = None,
21 *,
22 min: Optional[int] = None,
23 max: Optional[int] = None,
24 warning: bool = False,
25 ) -> None:
26 """
27 Asserts that the alignment width (the number of bases in the sequences) meets the specified criteria.
29 Args:
30 length (int, optional): If set, then alignment width must be equal to this value. Defaults to None.
31 min (int, optional): If set, then alignment width must be equal to or greater than this value. Defaults to None.
32 max (int, optional): If set, then alignment width must be equal to or less than this value. Defaults to None.
33 warning (bool): If True, raise a warning instead of an exception. Defaults to False.
34 This flag can be set by running this method with the prefix `warn_` instead of `assert_`.
35 """
36 alignment_width = self.get_alignment_length()
37 summary = f"The width of the alignment is {alignment_width}."
39 if width is not None:
40 assert_or_warn(
41 alignment_width == width,
42 warning,
43 summary,
44 f"This is not equal to the required width of {width}.",
45 )
46 if min is not None:
47 assert_or_warn(
48 alignment_width >= min,
49 warning,
50 summary,
51 f"This is less than the minimum width of {min}.",
52 )
53 if max is not None:
54 assert_or_warn(
55 alignment_width <= max,
56 warning,
57 summary,
58 f"This is greater than the maximum width of {max}.",
59 )
61 def assert_length(
62 self,
63 length: Optional[int] = None,
64 *,
65 min: Optional[int] = None,
66 max: Optional[int] = None,
67 warning: bool = False,
68 ) -> None:
69 """
70 Asserts that the alignment length (the number of sequences in the alignment) meets the specified criteria.
72 Args:
73 length (int, optional): If set, then alignment length must be equal to this value. Defaults to None.
74 min (int, optional): If set, then alignment length must be equal to or greater than this value. Defaults to None.
75 max (int, optional): If set, then alignment length must be equal to or less than this value. Defaults to None.
76 warning (bool): If True, raise a warning instead of an exception. Defaults to False.
77 This flag can be set by running this method with the prefix `warn_` instead of `assert_`.
78 """
79 alignment_length = len(self)
80 summary = f"The number of sequences in the alignment is {alignment_length}."
82 if length is not None:
83 assert_or_warn(
84 alignment_length == length,
85 warning,
86 summary,
87 f"This is less than required number of {length}.",
88 )
89 if min is not None:
90 assert_or_warn(
91 alignment_length >= min,
92 warning,
93 summary,
94 f"This is less than the minimum {min}.",
95 )
96 if max is not None:
97 assert_or_warn(
98 alignment_length <= max,
99 warning,
100 summary,
101 f"This is greater than the maximum {max}.",
102 )