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Run BLASTn

Source: R/get_blast_results.R
get_blast_results.Rd

Retrieve BLAST results from a given ASV

Usage

get_blast_results(
  asv,
  db_path,
  num_threads,
  blast_type = "blastn",
  perc_id = 80,
  perc_qcov_hsp = 80,
  num_alignments = 4,
  verbose = FALSE,
  env_name = "blast-env"
)

Arguments

asv

Vector of sequences to be BLASTed.

db_path

Complete path do formatted BLAST database.

num_threads

Number of threads to run BLAST on. Passed on to BLAST+ argument -num_threads.

blast_type

One of the available BLAST+ search engines, #' one of: c("blastn", "blastp", "blastx", "tblastn", "tblastx").

perc_id

Lowest identity percentage cutoff. Passed on to BLAST+ -perc_identity.

perc_qcov_hsp

Lowest query coverage per HSP percentage cutoff. Passed on to BLAST+ -qcov_hsp_perc.

num_alignments

Number of alignments to retrieve from BLAST. Max = 6.

verbose

Should condathis::run() internal command be shown?

env_name

The name of the conda environment with the parameter (i.e. "blast-env")

Value

A tibble with the results of BLASTn for each sequence.

Examples

if (FALSE) { # \dontrun{
blast_res <- BLASTr::get_blast_results(
  asv = "CTAGCCATAAACTTAAATGAAGCTATACTAAACTCGTTCGCCAGAGTA
  CTACAAGCGAAAGCTTAAAACTCATAGGACTTGGCGGTGTTTCAGACCCAC",
  db_path = "/data/databases/nt/nt",
  perc_id = 80,
  num_thread = 1,
  perc_qcov_hsp = 80,
  num_alignments = 2
)
} # }