fasta-filter

Filter a FASTA file and output a subset of the records on STDOUT

Usage

Filter a FASTA file and output a subset of the records on STDOUT

Usage: fasta-filter [OPTIONS] [FILE]

Arguments:
  [FILE]

Options:
  -c, --count <COUNT>
  -p, --pattern <PATTERN>
  -x, --exclude
  -m, --min <MIN>
  -n, --max <MAX>
  -h, --help               Print help
  -V, --version            Print version

This simple program expects to read FASTA data either on STDIN or from a named file, and will output a subset of the records to STDOUT. If -c or --count is specified, the first COUNT sequences present in the input will be used, after other filters are applied. Thus, at most COUNT sequences will be output (fewer if the file doesn't contain that many sequences after other filters are applied). Filtering can be based on a min or max length of sequence to include, as well as a pattern that either must or must not (-x) be present in the header of a record to include.

Example: fasta-filter --min 5 --max 2000 --pattern "mol:protein" test.fasta