validate_seq: Sequence validator

In bioseq: A Toolbox for Manipulating Biological Sequences

Sequence validator

Description

Validate character strings before sequence construction.

Usage

validate_seq(x, alphabet, invalid_replacement, type = "DNA")

Arguments

x	a character vector.
alphabet	a character vector defining the sequence alphabet;
invalid_replacement	a character to replace non valid characters
type	type of sequence ("DNA", "RNA", "AA"). It is only used to provide more informative warning messages.

Details

Validation steps:

1. Check that x is a character vector, fails if not.

2. Force alpha characters to uppercase

3. Delete blank characters (spaces and tabs)

4. Delete line breaks

5. Converts . (dots) to - (as both can represent a gap)

6. Replace invalid characters with N/X (with a warning).

Value

A character vector.

bioseq documentation built on Sept. 6, 2022, 5:07 p.m.