choose_best_assembly: Best Assembly

In selkamand/utilitybeltrefseq: What the Package Does (One Line, Title Case)

Best Assembly

Description

Best Assembly

Usage

choose_best_assembly(
  taxid_of_interest,
  intraspecific_filter = NA,
  break_ties_based_on_newest_sequence_added = TRUE,
  return_accession_only = TRUE,
  refseq_data_frame = load_refseq_data_frame_from_cache(),
  log_chosen_assembly = TRUE,
  logtitle = paste0("best_assembly_for_taxid_", taxid_of_interest, ".txt")
)

Arguments

taxid_of_interest	taxonomyID (int)
intraspecific_filter	e.g. 'strain=Raji'. For options look at the infraspecific_name column of the refseq_data_frame (string)
break_ties_based_on_newest_sequence_added	if we cant decide which is the best ref to use because they;re so similar - just pick the most recently uploaded sequence
return_accession_only	Return just the best assembly accession. If false will return a dataframe with accession ID plus lots of other info (bool)
refseq_data_frame	from load_refseq_data_frame_from_cache()
log_chosen_assembly	should we log details of chosen assembly to a file in addition to printing the results
logtitle	title of logfile (best_assembly_for_taxid_taxid.txt")

Value

if return_accession_only=TRUE then best assembly accession (string). Otherwise returns dataframe with accession ID of best assembly plus lots of other info (bool)

selkamand/utilitybeltrefseq documentation built on July 7, 2022, 7:35 a.m.