rammappy.sketch¶
Minimizer
¶
Represents a k-mer sketch (minimizer, syncmer, etc.).
Contains the genomic coordinate and the hash value.
Attributes:
| Name | Type | Description |
|---|---|---|
x |
int
|
The 64-bit integer combining the genomic coordinate and other metadata. |
y |
int
|
The 64-bit hash value of the k-mer. |
MinimizerSketcher
¶
A sketcher that extracts minimizers from sequences.
Minimizers are the lexicographically smallest k-mers in a sliding window of size w.
Examples:
>>> from rammappy.sketch import MinimizerSketcher
>>> sketcher = MinimizerSketcher(k=15, w=10)
>>> sketcher.sketch(b"ATGCGTACGATCGATC")
[<Minimizer object at ...>, ...]
__new__(*args, **kwargs)
builtin
¶
Create and return a new object. See help(type) for accurate signature.
RandstrobeSketcher
¶
A sketcher that extracts randstrobes from sequences.
Randstrobes are combinations of k-mers that provide more resilient matching.
Examples:
>>> from rammappy.sketch import RandstrobeSketcher
>>> sketcher = RandstrobeSketcher(k=15, w_min=10, w_max=30)
>>> sketcher.sketch(b"ATGCGTACGATCGATC")
[<Minimizer object at ...>, ...]
__new__(*args, **kwargs)
builtin
¶
Create and return a new object. See help(type) for accurate signature.
SyncmerSketcher
¶
A sketcher that extracts syncmers from sequences.
Syncmers provide a more evenly spaced sampling of sequences compared to minimizers.
Examples:
>>> from rammappy.sketch import SyncmerSketcher
>>> sketcher = SyncmerSketcher(k=15, s=5)
>>> sketcher.sketch(b"ATGCGTACGATCGATC")
[<Minimizer object at ...>, ...]
__new__(*args, **kwargs)
builtin
¶
Create and return a new object. See help(type) for accurate signature.