read_templates_single: Input of a Single Template File.
In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

read_templates_single

R Documentation

Input of a Single Template File.

Description

Read template sequences from a FASTA or CSV file.

Usage

read_templates_single(
  template.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

`template.file`	Path to a FASTA or CSV file containing the template sequences.
`hdr.structure`	A character vector 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.

Details

When supplying a FASTA file with template sequences, the input arguments hdr.structure, delim, id.column, rm.keywords, remove.duplicates, fw.region, rev.region, gap.character, and run are utilized. Most importantly, hdr.structure and delim should match the FASTA header structure. When supplying a CSV file with template sequences, the data are loaded without any modification and the CSV file should represent an object of class Templates, which can be stored using the write_templates function.