Class: Ms::Random::Fasta

Inherits:
Tap::Task
  • Object
show all
Defined in:
lib/ms/random/fasta.rb

Overview

:startdoc::task selects n random fasta entries

Selects random fasta entries from a fasta file. Entries are returned as an array, and by default as Ms::Fasta::Entry objects.

Instance Method Summary collapse

Instance Method Details

#process(fasta_file) ⇒ Object 



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# File 'lib/ms/random/fasta.rb', line 16

def process(fasta_file)
  entries = []

  log :index, fasta_file unless File.exist?("#{fasta_file}.index")
  Ms::Fasta::Archive.open(fasta_file) do |archive|
    total_entries = archive.length
    log :select, "#{n} entries"
  
    # pick entries, filtering by sequence
    while entries.length < n
      entry = archive[rand(total_entries)]
      next if distinct && entries.find {|existing| existing.sequence == entry.sequence }
    
      entries << entry
    end
  end

  entries.collect! do |entry|
    entry.to_s
  end if fasta

  entries
end