remove ids from a fasta file

remove_ids_from_fasta.rb

#!/usr/bin/env ruby
# usage: ruby remove_id_from_fasta.rb FILE_WITH_IDS FASTA_FILE

require 'bio'

ids = []
File.foreach(ARGV.shift, chomp: true) do |line|
 ids << line
end

Bio::FlatFile.auto(ARGF) do |ff|
  ff.each do |entry|
      puts entry.seq.to_fasta(entry.definition) unless ids.include?(entry.entry_id)
  end
end