Contents

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

Signal.trap('PIPE', 'EXIT')
Signal.trap('INT', 'EXIT')
root_cmd = Cri::Command.new_basic_root.modify do
  name 'peptfilter'
  summary 'Filter peptides based on specific criteria.'
  usage 'peptfilter [options]'
  description <<-EOS
  The peptfilter command filters a list of peptides according to specific criteria. The command expects a list of peptides that are passed

  - as separate command line arguments

  - in one or more text files that are passed as an argument to the -i option

  - to standard input

  The command will give priority to the first way peptides are passed, in the order as listed above. Text files and standard input should have one peptide per line. FASTA headers are preserved in the output, so that peptides remain bundled.
  EOS
  # flag :u, :unique, "filter duplicate peptides."
  required nil, :minlen, 'only retain tryptic peptides that have at least min (default: 5) amino acids.'
  required nil, :maxlen, 'only retain tryptic peptides that have at most max (default: 50) amino acids.'
  required :l, :lacks, 'only retain tryptic peptides that lack all amino acids from the string of residues.'
  required :c, :contains, 'only retain tryptic peptides that contain all amino acids from the string of residues.'
  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
    $stdin.each_line do |pept|
      # FASTA headers
      if pept.start_with? '>'
        puts pept
        next
      end
      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

      if length_ok && lacks_ok && contains_ok
        puts pept
      end
    end
  end
end

root_cmd.run(ARGV)

Version data entries

2 entries across 2 versions & 1 rubygems

Version	Path
unipept-0.7.1	bin/peptfilter
unipept-0.7.0	bin/peptfilter