metacoder (version 0.3.7)

parse_seq_input: 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
)

Value

A named character vector of sequences

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".