Find the ORF coverage

ORF_coverage.rb

require 'bio'

def analyse_input_file(input_file)
  overall_results = []
  biofastafile = Bio::FlatFile.open(Bio::FastaFormat, input_file)
  biofastafile.each_entry do |entry|
    overall_results << analyse_orfs(entry.entry_id, entry.naseq)
  end
  overall_results
end

def analyse_orfs(query_id, seq)
  results = {}
  orfs = get_orfs(seq)
  longest_orf       = orfs.sort_by { |_key, hash| hash[:coverage] }.last
  longest_orf_frame = longest_orf[1][:frame]
  coverage          = longest_orf[1][:coverage]
  translated_length = longest_orf[1][:translated_length]
  results[query_id] = {coverage: coverage, 
                       longest_orf_frame: longest_orf_frame, 
                       translated_length: translated_length}
  overall_results
end

def get_orfs(seq, min_length)
  result     = {}
  key        = 0
  min_length = min_length.to_i
  (1..6).each do |f|
    s = seq.translate(f)
    s.scan(/(\w{#{min_length},})/) do |_orf|
      orf_start = $~.offset(0)[0] + 1
      orf_end   = $~.offset(0)[1] + 1
      coverage = (((orf_end - orf_start) / s.length.to_f) * 100).ceil
      translated_length = s.length
      key += 1
      result[key] = { frame: f, 
                      orf_start: orf_start, 
                      orf_end: orf_end,
                      coverage: coverage,
                      translated_length: translated_length }
    end
  end
  result
end

input_file = ARGV[0]

puts analyse_input_file(input_file)