run_primersearch: Execute EMBOSS Primerseach

Description Usage Arguments Value See Also

Description

Execute EMBOSS Primerseach

Usage

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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.

See Also

parse_primersearch



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