parse_seq_input

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Read sequences in an unknown format

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

Keywords
internal
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

Aliases
  • parse_seq_input
Documentation reproduced from package metacoder, version 0.3.4, License: GPL-2 | GPL-3

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