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Functions to select sequence subsamples based on different weighting methods #11

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kelly-sovacool opened this issue Sep 11, 2020 · 0 comments

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kelly-sovacool commented Sep 11, 2020 •

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Input: fasta, count, and/or dist file.
Params: weighting method (by abundance, by distance, or simple random sample); fraction or number of sequences to select.
Output: list of accession numbers selected (could be written to accnos file to then give to mothur get.seqs).

Already implemented in Python for the OptiFit benchmarking project. Want to re-write it in R and write tests. The mothur sub.sample command doesn't have a weighting parameter.

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