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Write sharded NCBI genome download inputs

Source: R/ncbi_genomes.R
BascetPrepareNcbiGenomeFetchLists.Rd

BascetPrepareNcbiGenomeFetchLists() filters/normalizes an NCBI assembly metadata table and writes one TSV input shard per Bascet download job. The generated shards contain cell_id, assembly_accession, and ftp_path.

Usage

BascetPrepareNcbiGenomeFetchLists(
  assemblies,
  bascetRoot,
  outputName = "tofetch",
  numShards = NULL,
  genomesPerShard = 1000,
  latest = TRUE,
  excludeFromRefseq = TRUE,
  assemblyLevel = NULL,
  refseqCategory = NULL,
  overwrite = FALSE
)

Arguments

assemblies

Assembly metadata data frame, or path to assembly_summary.txt.

bascetRoot

The root folder where all Bascets are stored.

outputName

Name of output shard prefix.

numShards

Number of TSV shards to create. If NULL, derived from genomesPerShard.

genomesPerShard

Target number of genomes per shard when numShards is NULL.

latest

Keep only rows where version_status == "latest".

excludeFromRefseq

Keep only rows where excluded_from_refseq is empty.

assemblyLevel

Optional assembly levels to keep.

refseqCategory

Optional RefSeq categories to keep.

overwrite

Overwrite existing output files.

Value

A data frame describing genome-to-shard assignment.