pycall.rb 1.0.1 example to call Biopython SeqIO

try01-seqio.rb

#!/usr/bin/env ruby
# coding: utf-8

#
# Test data must be downloaded via:
# $ wget http://togows.org/entry/ncbi-nucleotide/J00231.fasta
#
# References: http://qiita.com/sato32ha6/items/6b762b0d0314a5db7dc3

require "pycall/import"
include PyCall::Import

pyfrom 'Bio', import: :SeqIO

module WrapGenerator
  def each
    iter = self.__iter__
    while true
      begin
        v = iter.__next__
      rescue PyCall::PyError
        break
      end
      yield v
    end
    self
  end
end

sio = SeqIO.parse("J00231.fasta", "fasta")
sio.extend(WrapGenerator)

sio.each do |record|
  id = record.id
  desc = record.description
  seq = PyCall.builtins.str.(record.seq)

  print 'id: <', id.class, '> ', id.inspect, "\n"
  print 'description: <', desc.class, '> ', desc.inspect, "\n"
  print 'seq: <', record.seq.inspect, '> ', seq.inspect, "\n"
end