run_primersearch: Execute EMBOSS Primersearch

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Execute EMBOSS Primersearch

Description

Execute EMBOSS Primersearch

Usage

run_primersearch(
  seq_path,
  primer_path,
  mismatch = 5,
  output_path = tempfile(),
  program_path = "primersearch",
  ...
)

Arguments

seq_path	A character vector of length 1. The path to the fasta file containing reference sequences to search for primer matches in.
primer_path	A character vector of length 1. The path to the file containing primer pairs to match. The file should be whitespace-delimited with 3 columns: primer name, first primer sequence, and second primer sequence.
mismatch	An integer vector of length 1. The percentage of mismatches allowed.
output_path	A character vector of length 1. Where the output of primersearch is saved.
program_path	A character vector of length 1. The location of the primersearch binary. Ideally, it should be in your system's search path.
...	Additional arguments are passed to primersearch.

Value

The command generated as a character vector of length 1.

See Also

parse_primersearch

metacoder documentation built on April 4, 2023, 9:08 a.m.