mask

Masks the sequence within a given range or comma delimited list of ranges by converting to lowercase (soft mask) or replacing with a character (hard masking). Reverting soft masking is also possible.

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

Options:
    <range>             Range in the form 'start..end' or 'start..' or '..end',
                        Variables containing one range bound or the whole range
                        are possible.
    --hard <C>          Do hard masking instead of soft masking, replacing
                        everything in the range(s) with the given character
    --unmask            Unmask (convert to uppercase instead of lowercase)
    -e, --exclude       Exclusive range: excludes start and end positions
                        from the masked sequence.
    -0                  Interpret range as 0-based, with the end not included.

See this page for the options common to all commands.

Description

Masking ranges are 1-based, using negative numbers means that the number is relative to the sequence end (see the explanation of ranges with basic examples). A comma delimited list of ranges can be supplied, which may contain variables, or the whole range may be a variable.

st find -r -a rng={f:drange:all} [AG]GA seqs.fa \
  | st mask a:rng