bio.seq

Source code: bio/seq.seq

type bio.seq.BaseCounts

Representation of base counts of a sequence

Magic methods:

__init__()

Base counts of empty sequence (i.e. all zero)

__add__(other: BaseCounts)

Adds corresponding base counts

__sub__(other: BaseCounts)

Subtracts corresponding base counts

__str__()

Methods:

add(A: bool = False, C: bool = False, G: bool = False, T: bool = False, N: bool = False)

Increments the specified base counts

extension seq

Properties:

bases

BaseCount for this sequence

Magic methods:

__init__(s: str)

__init__()

__eq__(other: seq)

__ne__(other: seq)

__lt__(other: seq)

__le__(other: seq)

__gt__(other: seq)

__ge__(other: seq)

__str__()

__contains__(other: seq)

__len__()

__bool__()

__hash__()

__getitem__(idx: int)

__getitem__(s: slice)

__getitem__(s: lslice)

__getitem__(s: rslice)

__getitem__(s: eslice)

__copy__()

__iter__()

__reversed__()

__int__()

__invert__()

Reverse complemented sequence

__reversed__()

Methods:

split(k: int, step: int = 1)

Iterator over length-k subsequences of the given sequence with the specified step size.

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.

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.

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.

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.

N()

Returns whether this sequence contains ambiguous bases. An ambiguous base is defined to be a non-ACGT base.