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oxli-bio / oxli

k-mers and the like
BSD 3-Clause "New" or "Revised" License
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Load kmer counts from file #77

Open Adamtaranto opened 1 month ago

Adamtaranto commented 1 month ago

oxli is currently slower than other counters for large genomes. Suggest option to bulk load kmer counts from another counter i.e. Jellyfish via text dump.

Would allow users to load pre-calculated counts for use with oxli's python API.

@ctb what do you reckon?

Adamtaranto commented 2 days ago

The other option is for users to use the Python API to manually set the counts i.e. kct[kmer] = count.

Only advantage of adding a method to load counts from a dump file is that we could make it multithreaded.