iupac2regex: Ambiguity symbol conversion

In microseq: Basic Biological Sequence Handling

Ambiguity symbol conversion

Description

Converting DNA ambiguity symbols to regular expressions, and vice versa.

Usage

iupac2regex(sequence)
regex2iupac(sequence)

Arguments

sequence

Character vector containing DNA sequences.

Details

The DNA alphabet may contain ambiguity symbols, e.g. a W means either A or T. When using a regular expression search, these letters must be replaced by the proper regular expression, e.g. W is replaced by [AT] in the string. The iupac2regex makes this translation, while regex2iupac converts the other way again (replace [AT] with W).

Value

A string where the ambiguity symbol has been replaced by a regular expression (iupac2regex) or a regular expression has been replaced by an ambiguity symbol (regex2iupac).

Author(s)

Lars Snipen.

Examples

iupac2regex("ACWGT")
regex2iupac("AC[AG]GT")

microseq documentation built on Aug. 21, 2023, 5:10 p.m.