read_templates_fasta: Input of Template Sequences.

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Input of Template Sequences.

Description

Read template sequences from a FASTA file.

Usage

read_templates_fasta(
  fasta.file,
  hdr.structure = NULL,
  delim = NULL,
  id.column = NULL,
  rm.keywords = NULL,
  remove.duplicates = FALSE,
  fw.region = c(1, 30),
  rev.region = c(1, 30),
  gap.character = "-",
  run = NULL
)

Arguments

fasta.file	Path to a FASTA file containing the template sequences.
hdr.structure	Names describing the information contained in the FASTA headers. In case that the headers of fasta.file contain template group information, please include the keyword "GROUP" in hdr.structure.
delim	Delimiter for the information in the FASTA headers.
id.column	Field in the header to be used as the identifier.
rm.keywords	A vector of keywords that are used to remove templates whose headers contain any of the keywords.
remove.duplicates	Whether duplicate sequence shall be removed.
fw.region	The positional interval from the template 5' end specifying the binding sites for forward primers.
rev.region	The positional interval from the template 3' end specifying the binding sites for reverse primers.
gap.character	The character in the input file representing gaps. Gaps are automatically removed upon input.
run	An identifier for the template sequences.

Value

An object of class Templates.

Examples

fasta.file <- system.file("extdata", "IMGT_data", "templates", 
              "Homo_sapiens_IGH_functional_exon.fasta", package = "openPrimeR")
hdr.structure <- c("ACCESSION", "GROUP", "SPECIES", "FUNCTION")
template.df <- read_templates(fasta.file, hdr.structure, "|", "GROUP")

matdoering/openPrimeR documentation built on July 4, 2025, 3:59 a.m.