bio.seq¶
Source code: bio/seq.seq
- class bio.seq.seq¶
Magic methods:
- class bio.seq.BaseCounts¶
Representation of base counts of a sequence
Magic methods:
- __new__()
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:
- __new__(s: str)
- __new__()
- __eq__(other: seq)
- __ne__(other: seq)
- __to_py__()
- __from_py__(s: pyobj)
- __lt__(other: seq)
- __le__(other: seq)
- __gt__(other: seq)
- __ge__(other: seq)
- __str__()
- __contains__(other: seq)
- __contains__[K](kmer: K)
- __len__()
- __bool__()
- __hash__()
- __getitem__(idx: int)
- __getitem__(s: Slice)
- __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.