sort

Sort records by sequence or any other criterion

The sort key can be 'seq', 'id', or any variable/function, expression, or text containing them (see help and st sort --help-vars).

Records with identical keys are kept in input order.

The actual value of the key is available through the 'key' variable. It can be written to a header attribute or TSV field.

Usage: st sort [OPTIONS] <KEY> [INPUT]...

Options:
  -h, --help  Print help (see more with '--help')

'Sort' command options:
  -r, --reverse              Sort in reverse order
  -M, --max-mem <SIZE>       Maximum amount of memory (approximate) to use for
                             sorting. Either a plain number (bytes) a number
                             with unit (K, M, G, T) based on powers of 2
                             [default: 5G]
      --temp-dir <PATH>      Path to temporary directory (only if memory limit
                             is exceeded)
      --temp-file-limit <N>  Maximum number of temporary files allowed [default:
                             1000]
  <KEY>                  The key used to sort the records. It can be a single
                         variable/function such as 'seq', 'id', a composed
                         string, e.g. '{id}_{desc}', or a comma-delimited list
                         of multiple variables/functions to sort by, e.g.
                         'seq,attr(a)'. In this case, the records are first
                         sorted by sequence, but in case of identical sequences,
                         records are sorted by the header attribute 'a'

See this page for the options common to all commands.

More

This page lists more examples with execution times and comparisons with other tools.

Variables provided by the 'sort' command

key	The value of the key used for sorting

Example

Sort by part of the sequence ID, which is obtained using a JavaScript expression. We additionally keep this substring by writing the sort key to a header attribute::

st sort -n '{ id.slice(2, 5) }' -a id_num='{num(key)}' input.fasta

>id001 id_num=1
SEQ
>id002 id_num=2
SEQ
(...)