blast_n: Run a blastn query.

In joelnitta/baitfindR: Find Baits for Sequence Capture

Description

This is a wrapper for blastn.

Usage

blast_n(
  query,
  database,
  out_file = NULL,
  outfmt = "6",
  other_args = NULL,
  echo = TRUE,
  wd,
  ...
)

Arguments

query	Character vector of length one; the path to the fasta file to use as the query sequence(s).
database	Character vector of length one; the name of the blast database.
out_file	Character vector of length one; the name to use for the results file.
outfmt	Character vector of length one; value to pass to blastn outfmt argument. Default = "6".
other_args	Character vector; other arguments to pass on to blastn. Must be formatted so that each argument name and its value are separate, consecutive elements of the vector, e.g., c("-evalue", 10, "-num_threads", 1). The argument name must be preceded by a hyphen. For a list of options, run blastn -help.
echo	Logical; should standard error and output be printed?
wd	Character vector of length one; working directory. The blast search will be conducted here.
...	Additional other arguments. Not used by this function, but meant to be used by drake_plan for tracking during workflows.

Value

A tab-separated text file with the results of the blastn search, named with the value of out_file.

Author(s)

Joel H Nitta, [e-mail]

References

https://www.ncbi.nlm.nih.gov/books/NBK279690/

Examples

library(ape)

# Make temp dir for storing files
temp_dir <- fs::dir_create(fs::path(tempdir(), "baitfindR_example"))

# Write out ape::woodmouse dataset as DNA
data(woodmouse)
ape::write.FASTA(woodmouse, fs::path(temp_dir, "woodmouse.fasta"))

# Make blast database
build_blast_db(
  fs::path(temp_dir, "woodmouse.fasta"),
  db_type = "nucl",
  out_name = "wood",
  parse_seqids = TRUE,
  wd = temp_dir)

# Blast the original sequences against the database
blast_n(
  fs::path(temp_dir, "woodmouse.fasta"),
  database = "wood",
  out_file = "blastn_results",
  wd = temp_dir,
  echo = TRUE
)

# Take a look at the results.
readr::read_tsv(
  fs::path(temp_dir, "blastn_results"),
  col_names = FALSE
  )

# Cleanup.
fs::file_delete(temp_dir)

joelnitta/baitfindR documentation built on May 7, 2020, 6:21 p.m.