mask

Soft or hard mask sequence ranges

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] <RANGES> [INPUT]...

Options:
  -h, --help  Print help

'Mask' command options:
      --hard <CHAR>  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, --exclusive    Exclusive range: excludes start and end positions from the
                     masked sequence. In the case of unbounded ranges (`start:`
                     or `:end`), the range still extends to the complete end or
                     the start of the sequence
  -0, --zero-based   Interpret range as 0-based, with the end not included
  <RANGES>       Range in the form 'start:end' or 'start:' or ':end', The range
                 start/end may be defined by varialbes/functions, or the
                 varialbe/function may contain a whole range

See this page for the options common to all commands.

A comma delimited list of ranges can be supplied, which may contain variables, or the whole range may be a variable.

Masking ranges always include the start and end coordinates unless -0 is specified. Coordinates can be negative to indicate an offset from the end. See explanation of ranges for more details.

Example

In this example, we search all occurrences of a pattern using a regular expression with the find command and store them as comma-delimited list using match_range(all):

st find -r -a rng='{match_range(all)}' '[AG]GA' input.fasta \
  | st mask 'attr(rng)'

Possible output:

>seq1 rng=6:8,14:16
AGTTAagaCTTAAggaT
(...)