Functions to select sequence subsamples based on different weighting methods - Githubissues

SchlossLab / schtools

Schloss Lab Tools for Reproducible Microbiome Research 💩

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

Open kelly-sovacool opened 4 years ago

kelly-sovacool commented 4 years ago

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.