# run_primersearch

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Percentile

##### Execute EMBOSS Primerseach

Execute EMBOSS Primerseach

Keywords
internal
##### Usage
run_primersearch(seq_path, primer_path, mismatch = 5, output_path = tempfile(), program_path = "primersearch", dont_run = FALSE, ...)
##### 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.
dont_run
If TRUE, the command is generated, but not executed. This could be useful if you want to execute the command yourself.
...
Additional arguments are passed to primersearch.
##### Value

The command generated as a character vector of length 1.

parse_primersearch