Contents

#!/usr/bin/env ruby
require 'cri'

root_cmd = Cri::Command.new_basic_root.modify do
  name 'peptfilter'
  flag :i, :unique, "only output unique peptides"
  required :l, :minlen, "minimum length (default: 5)"
  required :u, :maxlen, "minimum length (default: 50)"
  required :a, :lacks, "a string whose letters represent amino acids that may not occur in the peptide"
  required :c, :contains, "a string whose letters represent amino acids that must all occur in the peptide"
  run do |opts, args, cmd|
    minlen = opts.fetch(:minlen, "5").to_i
    maxlen = opts.fetch(:maxlen, "50").to_i
    lacks = opts.fetch(:lacks, "").chars.to_a
    contains = opts.fetch(:contains, "").chars.to_a
    filtered = $stdin.readlines.select do |pept|
      pept = pept.chomp
      length_ok = pept.length >= minlen && pept.length <= maxlen
      lacks_ok = (pept.chars.to_a & lacks).size == 0
      contains_ok = (pept.chars.to_a & contains).size == contains.size

      length_ok && lacks_ok && contains_ok
    end
    if opts[:unique]
      puts filtered.uniq
    else
      puts filtered
    end
  end
end

root_cmd.run(ARGV)

Version data entries

3 entries across 3 versions & 1 rubygems

Version	Path
unipept-0.2.6	bin/peptfilter
unipept-0.2.5	bin/peptfilter
unipept-0.2.4	bin/peptfilter