bio.kmer¶
Source code: bio/kmer.seq
- extension Kmer[k]¶
Magic methods:
- __new__()
- __new__(kmer: Kmer[k])
- __new__(p: Ptr[byte], L: int, b: bool)
- __new__(s: seq)
- __new__(s: seq, rc: bool)
- __new__(s: seq)
- __new__(s: str)
- __new__(n: int)
- __int__()
- __copy__()
- __invert__()
- __getitem__(idx: int)
- __lshift__(s: seq)
- __rshift__(s: seq)
- __sub__(other: Kmer[k])
- Hamming distance algorithm:
input: kmer1, kmer2 mask1 = 0101…0101 (same bit width as encoded kmer) mask2 = 1010…1010 (same bit width as encoded kmer) popcnt(
(((kmer1 & mask1) ^ (kmer2 & mask1)) << 1) | ((kmer1 & mask2) ^ (kmer2 & mask2))
)
- __hash__()
- __len__()
- __eq__(other: Kmer[k])
- __ne__(other: Kmer[k])
- __lt__(other: Kmer[k])
- __gt__(other: Kmer[k])
- __le__(other: Kmer[k])
- __ge__(other: Kmer[k])
- __contains__(s: seq)
- __str__()
- __pickle__(jar: Jar)
- __unpickle__(jar: Jar)
- __match__(pattern: str)
Methods: