Reformat BLASTn results

Usage

blastn_results(
  results_table,
  bam_file,
  num_results = 10,
  num_reads_per_result = 100,
  hit_list = 10,
  num_threads = 1,
  db_path,
  out_path,
  db = NULL,
  sample_name = NULL,
  quiet = quiet,
  accession_path,
  fasta_dir = NULL,
  BPPARAM
)

Arguments

results_table: data.frame containing the MetaScope results.
bam_file: Rsamtools::bamFile instance for the given sample.
num_results: Integer; maximum number of Metascope results to BLAST. Default is 10.
num_reads_per_result: Integer; number of reads to BLAST per result. Default is 100.
hit_list: Integer; how many BLAST results to fetch for each read. Default is 10.
num_threads: Integer; how many threads to use if multithreading. Default is 1.
db_path: Character string; filepath for the location of the pre-installed BLAST database.
out_path: Character string; Output directory to save CSV output files, including base name of files. For example, given a sample "X78256", filepath would be file.path(directory_here, "X78256") with extension omitted.
db: Currently accepts one of c("ncbi", "silva", "other") Default is "ncbi", appropriate for samples aligned against indices compiled from NCBI whole genome databases. Alternatively, usage of an alternate database (like Greengenes2) should be specified with "other".
sample_name: Character string, sample name for output files.
quiet: Logical, whether to print out more informative messages. Default is FALSE.
accession_path: (character) Filepath to NCBI accessions SQL database. See taxonomzr::prepareDatabase().
fasta_dir: Character string; Directory where fastas from metascope_id are stored.
BPPARAM: An optional BiocParallelParam instance determining the parallel back-end to be used during evaluation.

Value

Creates and exports num_results number of csv files with blast results from local blast