# run_primersearch

0th

Percentile

##### Execute EMBOSS Primersearch

Execute EMBOSS Primersearch

Keywords
internal
##### 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.

parse_primersearch