blastn_results: Reformat BLASTn results

In compbiomed/MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

Reformat BLASTn results

Description

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

compbiomed/MetaScope documentation built on Jan. 16, 2025, 10:23 p.m.