Run BLASTn — get_blast_results • BLASTr

Retrieve BLAST results from a given ASV

Usage

get_blast_results(
  asv,
  db_path,
  num_threads = 1L,
  blast_type = "blastn",
  perc_id = 80L,
  perc_qcov_hsp = 80L,
  num_alignments = 4L,
  verbose = c("silent", "cmd", "output", "full"),
  env_name = "blastr-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 used to run command-line tools (i.e. "blastr-blast-env").

Value

A tibble with the results of BLASTn for each sequence.

Examples

if (FALSE) { # \dontrun{
dna_fasta_path <- fs::path_package(
  "BLASTr", "extdata", "minimal_db_blast",
  ext = "fasta"
)
temp_db_path <- fs::path_temp("minimal_db_blast")
make_blast_db(fasta_path = dna_fasta_path, db_path = temp_db_path)
asvs_string <- "CTAGCCATAAACTTAAATGAAGCTATACTAAACTCGTTCGCCAG
AGTACTACAAGCGAAAGCTTAAAACTCATAGGACTTGGCGGTGTTTCAGACCCAC"

get_blast_results(asv = asvs_string, db_path = temp_db_path)
} # }