bio.align
¶
Source code: bio/align.seq
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type
bio.align.
SubMat
¶ Substitution matrix for amino acid alignment
Magic methods:
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__init__
(d: dict[tuple[str, str], int]) Creates a SubMat from a dictionary mapping amino acid pairs to score values.
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__str__
()
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extension
CIGAR
¶ Properties:
Magic methods:
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extension
Alignment
¶ Properties:
Magic methods:
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__init__
()
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__init__
(cigar: str, score: int)
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__bool__
()
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extension
seq
¶ Magic methods:
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__matmul__
(other: seq) Performs Smith-Waterman alignment against another sequence. Mismatch and gap costs are 1 (Levenshtein distance).
Methods:
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align
(other: seq, a: int = 2, b: int = 4, ambig: int = 0, gapo: int = 4, gape: int = 2, gapo2: int = - 1, gape2: int = - 1, bandwidth: int = - 1, zdrop: int = - 1, end_bonus: int = 0, score_only: bool = False, right: bool = False, generic_sc: bool = False, approx_max: bool = False, approx_drop: bool = False, ext_only: bool = False, rev_cigar: bool = False, splice: bool = False, splice_fwd: bool = False, splice_rev: bool = False, splice_flank: bool = False)¶ Performs Smith-Waterman alignment against another sequence.
a: match score
b: mismatch score
ambig: ambiguous (i.e. N) match score
gapo: gap open cost
gape: gap extension cost
gapo2: 2nd gap open cost for dual gap cost function
gape2: 2nd gap extension cost for dual gap cost function
bandwidth: bandwidth for DP alignment
zdrop: off-diagonal drop-off to stop extension
end_bonus: score bonus for reaching end of DP matrix
score_only: if true, don’t compute CIGAR
right: if true, right-align gaps
approx_max: if true, approximate max
approx_drop: if true, approximate Z-drop
rev_cigar: if true, reverse CIGAR in output
ext_only: if true, perform extension alignment
splice: if true, perform spliced alignment
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extension
pseq
¶ Magic methods:
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__matmul__
(other: pseq) Performs Smith-Waterman alignment against another sequence. Uses Blosum-62, gap open cost 11 and gap extend cost 1.
Methods:
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align
(other: pseq, mat: SubMat, gapo: int = 4, gape: int = 2, gapo2: int = - 1, gape2: int = - 1, bandwidth: int = - 1, zdrop: int = - 1, end_bonus: int = 0, score_only: bool = False, right: bool = False, generic_sc: bool = False, approx_max: bool = False, approx_drop: bool = False, ext_only: bool = False, rev_cigar: bool = False)¶ Performs Smith-Waterman alignment against another sequence.
mat: score matrix
gapo: gap open cost
gape: gap extension cost
gapo2: 2nd gap open cost for dual gap cost function
gape2: 2nd gap extension cost for dual gap cost function
bandwidth: bandwidth for DP alignment
zdrop: off-diagonal drop-off to stop extension
end_bonus: score bonus for reaching end of DP matrix
score_only: if true, don’t compute CIGAR
right: if true, right-align gaps
approx_max: if true, approximate max
approx_drop: if true, approximate Z-drop
rev_cigar: if true, reverse CIGAR in output
ext_only: if true, perform extension alignment
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type
bio.align.
InterAlignParams
¶
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type
bio.align.
SeqPair
¶ Magic methods:
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__init__
(id: int, len1: int, len2: int, flags: int)
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