In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Loading primers

Existing sets of primers can also be loaded from FASTA files. Why don't you try loading the following primer FASTA file using read_primers() into the primer.df variable?

fasta.file <- system.file("extdata", "IMGT_data", "primers", 
        "IGHV", "Tiller2008_1st.fasta", package = "openPrimeR")

# Load the prmiers from 'fasta.file' into 'primer.df' and explore the data
fasta.file <- system.file("extdata", "IMGT_data", "primers", 
        "IGHV", "Tiller2008_1st.fasta", package = "openPrimeR")

# Load the prmiers from 'fasta.file' into 'primer.df' and explore the data
fasta.file <- system.file("extdata", "IMGT_data", "primers", 
        "IGHV", "Tiller2008_1st.fasta", package = "openPrimeR")
primer.df <- read_primers(fasta.file)
print(primer.df)

As we can see, the data frame only contains entries in the Forward, but not the Reverse column indicating that this is a set of forward primers only. Moreover, we obtain some basic information about the primers such as their length via primer_length_fw and their degeneracy via Degeneracy_fw. As a careful reader, you may now wonder how it was possible to annotate the primers with their directionalities without specifying any identifiers.

This was possible because the input FASTA file already provided the default keywords used by read_primers for identifying the directions of the primers, which you verify by finding that the tag _fw is shared by all entries in the ID column. For your own primers, it is crucial that you tag the directionality of the primers in the FASTA file correctly and then specify the respective keywords using the fw.id and rev.id arguments in case that you are deviating from the defaults, for example:

fasta.file <- system.file("extdata", "IMGT_data", "primers", 
        "IGHV", "Tiller2008_1st.fasta", package = "openPrimeR")
primer.df <- read_primers(fasta.file, fw.id = "_fw", rev.id = "_rev")