replace

This command does fast search and replace for patterns in sequences or ids/descriptions.

Usage:
    st replace [options][-a <attr>...][-l <list>...] <pattern> <replacement> [<input>...]
    st replace (-h | --help)
    st replace --help-vars

Options:
    <replacement>       Replacement string, cannot contain variables.
    -i, --id            Replace in IDs instead of sequences
    -d, --desc          Replace in descriptions
    -r, --regex         Interpret <pattern> as regular expression
    -t, --threads <N>   Number of threads [default: 1]

See this page for the options common to all commands.

Description

Example: Conversion of RNA to DNA by replacing all occurrences of U with T:

st replace U T rna.fa > dna.fa

Regular expression (regex) groups can be accessed with the '$' prefix in replacements.