batch_reduce_ncbi: Batch reduce NCBI tables

In fishsciences/metabarcode_utils: Meta-barcoding Utilities

Batch reduce NCBI tables

Description

Convenience function to batch process NCBI tables.

Usage

batch_extract_ncbi_tabs(
  file_dir,
  files = list.files(file_dir, pattern = "\\.txt$", full.names = TRUE, recursive =
    TRUE),
  ...
)

batch_reduce_ncbi(tab_list, accession_filter = c("all", "top"), out_dir, ...)

Arguments

file_dir	the directory to look for raw NCBI output files
files	vector, the full file path to the raw NCBI files
...	additional args passed to reduce_nbci
tab_list	a list of extracted tables created by batch_extract_ncbi_tabs
accession_filter	character, one of "all" to keep all accessions, or "top" to only keep the top accession.
out_dir	optional, if specified, the reduced tables will be written to CSV in the directory specified. If the directory does not exist, it will be created.

Value

list of reducded tables

Author(s)

Matt Espe

fishsciences/metabarcode_utils documentation built on Feb. 25, 2024, 11:31 a.m.