replace

Fast and simple pattern replacement in sequences or headers

Usage: st replace [OPTIONS] <PATTERN> <REPLACEMENT> [INPUT]...

Options:
  -h, --help  Print help

'Replace' command options:
  -i, --id           Replace in IDs instead of sequences
  -d, --desc         Replace in descriptions
  -r, --regex        Interpret pattern as a regular expression. Unicode
                     characters are supported when searching in
                     IDs/descriptions, but not for sequence searches
  -t, --threads <N>  Number of threads [default: 1]
  <PATTERN>          Search pattern
  <REPLACEMENT>      Replacement string, cannot contain variables

See this page for the options common to all commands.

Examples

RNA to DNA

Simple RNA to DNA conversion by replacing all occurrences of U with T:

st replace U T rna.fasta > dna.fasta

Regular expressions

The following command extracts Genbank accessions from sequence headers that follow the old-style Genbank format, e.g. gi|1031916024|gb|KU317675.1|:

st replace -ir "gi\|\d+\|[a-z]+\|(?<acc>.+?)\|.*" seqs.fasta '$acc' > seqs_accession.fasta

The accession KU317675.1 is matched by the named regex group 'acc' and referenced by '$acc'. Regular expression (regex) groups can be accessed with the '$' prefix in replacements.

You can use online tools such as https://regex101.com to build and debug your regular expression

⚠ In Bash, make sure to use single quotes around '$acc' (not double quotes) to avoid that $acc is interpreted as a shell variable.

More

This page lists examples with execution times compared to other tools.