This function creates the dada2 assignTaxonomy training fasta for the official Silva NR99 release files. If 'include.species'=TRUE, a 7th taxonomic level (species) will be added based on the Genus species binomial in the Silva taxonomy string, if present and valid.
## Silva release v138 path <- "~/tax/Silva/v138" dada2:::makeTaxonomyFasta_SilvaNR(file.path(path, "SILVA_138_SSURef_NR99_tax_silva.fasta.gz"), file.path(path, "tax_slv_ssu_138.txt"), "~/Desktop/silva_nr99_v138_train_set.fa.gz") dada2:::makeTaxonomyFasta_SilvaNR(file.path(path, "SILVA_138_SSURef_NR99_tax_silva.fasta.gz"), file.path(path, "tax_slv_ssu_138.txt"), include.species=TRUE, "~/Desktop/silva_nr99_v138_wSpecies_train_set.fa.gz")
makeTaxonomyFasta_SilvaNR( fin, ftax, fout, include.species = FALSE, compress = TRUE )
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