bio.seq¶
Source code: bio/seq.seq
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class
bio.seq.seq¶ Magic methods:
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class
bio.seq.BaseCounts¶ Representation of base counts of a sequence
Magic methods:
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__new__() Base counts of empty sequence (i.e. all zero)
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__add__(other: BaseCounts) Adds corresponding base counts
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__sub__(other: BaseCounts) Subtracts corresponding base counts
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__str__()
Methods:
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add(A: bool = False, C: bool = False, G: bool = False, T: bool = False, N: bool = False)¶ Increments the specified base counts
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extension
seq¶ Properties:
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bases¶ BaseCount for this sequence
Magic methods:
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__new__(s: str)
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__new__()
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__eq__(other: seq)
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__ne__(other: seq)
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__to_py__()
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__from_py__(s: pyobj)
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__lt__(other: seq)
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__le__(other: seq)
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__gt__(other: seq)
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__ge__(other: seq)
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__str__()
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__contains__(other: seq)
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__contains__[K](kmer: K)
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__len__()
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__bool__()
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__hash__()
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__getitem__(idx: int)
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__getitem__(s: Slice)
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__copy__()
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__iter__()
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__reversed__()
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__int__()
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__invert__() Reverse complemented sequence
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__reversed__()
Methods:
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split(k: int, step: int = 1)¶ Iterator over length-k subsequences of the given sequence with the specified step size.
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kmers[K](step: int = 1)¶ Iterator over k-mers (type K) of the given sequence with the specified step size. Note that k-mers spanning ambiguous bases will be skipped.
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kmers_canonical[K]()¶ Iterator over canonical k-mers (type K) of the given sequence. Note that k-mers spanning ambiguous bases will be skipped. A canonical k-mer is defined to be the minimum of a k-mer and its reverse complement.
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kmers_canonical_with_pos[K]()¶ Iterator over (0-based index, canonical k-mer) tuples of the given sequence with the specified step size. Note that k-mers spanning ambiguous bases will be skipped.
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kmers_with_pos[K](step: int = 1)¶ Iterator over (0-based index, k-mer) tuples of the given sequence with the specified step size. Note that k-mers spanning ambiguous bases will be skipped.
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N()¶ Returns whether this sequence contains ambiguous bases. An ambiguous base is defined to be a non-ACGT base.
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