cogent3_pykmertools: kmer counting plugins for cogent3
Installation
We recommend installing cogent3_pykmertools from PyPI as follows
pip install cogent3_pykmertools
Or using uv
uv pip install cogent3_pykmertools
The installation process registers the apps and plugins with cogent3.
The provided apps
pkt_count_kmers(): does what the name says! When this package is installed, this app will be used by thecogent3Sequence.count_kmers()andSequenceCollection.count_kmers()methods. This app can also be run in parallel, which can be useful if you have a lot of sequences in theSequenceCollection.pkt_kmer_header: returns the k-mers as strings, so you know what their order is.
Getting help on the apps
Use the cogent3.app_help() function. For example, cogent3.app_help("pkt_count_kmers").
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