parse_seq_input: Read sequences in an unknown format

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Read sequences in an unknown format

Description

Read sequences in an unknown format. This is meant to parse the sequence input arguments of functions like primersearch.

Usage

parse_seq_input(
  input = NULL,
  file = NULL,
  output_format = "character",
  u_to_t = FALSE
)

Arguments

input	(character) One of the following: A character vector of sequences See the example below for what this looks like. The parser read_fasta produces output like this. A list of character vectors Each vector should have one base per element. A "DNAbin" object This is the result of parsers like read.FASTA. A list of "SeqFastadna" objects This is the result of parsers like read.fasta. Either "input" or "file" must be supplied but not both.
file	The path to a FASTA file containing sequences to use. Either "input" or "file" must be supplied but not both.
output_format	The format of the sequences returned. Either "character" or "DNAbin".
u_to_t	If 'TRUE', then "U" in the sequence will be converted to "T".

Value

A named character vector of sequences

metacoder documentation built on April 4, 2023, 9:08 a.m.