3

Primer 3というコマンド ライン プログラムを実行しています。入力ファイルを受け取り、データを標準出力に返します。その入力を受け入れ、エントリをハッシュに入れるRubyスクリプトを作成しようとしています。

返された結果は以下のとおりです。「=」記号でデータを分割したいので、has は次のようになります。

{:SEQUENCE_ID => "example", :SEQUENCE_TEMPLATE => "GTAGTCAGTAGACNAT..etc", :SEQUENCE_TARGET => "37,21" etc }

また、キーを小文字にしたいと思います。

 {:sequence_id => "example", :sequence_template => "GTAGTCAGTAGACNAT..etc", :sequence_target => "37,21" etc }

これは私の現在のスクリプトです：

#!/usr/bin/ruby
puts 'Primer 3 hash'

primer3 = {}
while line = gets do
  name, height = line.split(/\=/)
  primer3[name] = height.to_i
end

puts primer3

これを返しています：

Primer 3 hash
{"SEQUENCE_ID"=>0, "SEQUENCE_TEMPLATE"=>0, "SEQUENCE_TARGET"=>37, "PRIMER_TASK"=>0,     "PRIMER_PICK_LEFT_PRIMER"=>1, "PRIMER_PICK_INTERNAL_OLIGO"=>1,  "PRIMER_PICK_RIGHT_PRIMER"=>1, "PRIMER_OPT_SIZE"=>18, "PRIMER_MIN_SIZE"=>15, "PRIMER_MAX_SIZE"=>21, "PRIMER_MAX_NS_ACCEPTED"=>1, "PRIMER_PRODUCT_SIZE_RANGE"=>75, "P3_FILE_FLAG"=>1, "SEQUENCE_INTERNAL_EXCLUDED_REGION"=>37, "PRIMER_EXPLAIN_FLAG"=>1, "PRIMER_THERMODYNAMIC_PARAMETERS_PATH"=>0, "PRIMER_LEFT_EXPLAIN"=>0, "PRIMER_RIGHT_EXPLAIN"=>0, "PRIMER_INTERNAL_EXPLAIN"=>0, "PRIMER_PAIR_EXPLAIN"=>0, "PRIMER_LEFT_NUM_RETURNED"=>0, "PRIMER_RIGHT_NUM_RETURNED"=>0, "PRIMER_INTERNAL_NUM_RETURNED"=>0, "PRIMER_PAIR_NUM_RETURNED"=>0, ""=>0}

情報源

SEQUENCE_ID=example
SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
PRIMER_TASK=pick_detection_primers
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_OPT_SIZE=18
PRIMER_MIN_SIZE=15
PRIMER_MAX_SIZE=21
PRIMER_MAX_NS_ACCEPTED=1
PRIMER_PRODUCT_SIZE_RANGE=75-100
P3_FILE_FLAG=1
SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
PRIMER_EXPLAIN_FLAG=1
PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/usr/local/Cellar/primer3/2.3.4/bin/primer3_config/
PRIMER_LEFT_EXPLAIN=considered 65, too many Ns 17, low tm 48, ok 0
PRIMER_RIGHT_EXPLAIN=considered 228, low tm 159, high tm 12, high hairpin stability 22, ok 35
PRIMER_INTERNAL_EXPLAIN=considered 0, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=

$ primer3_core < example2 | ruby /Users/sean/Dropbox/bin/rb/read_primer3.rb
4

3 に答える 3

4 
#!/usr/bin/ruby
puts 'Primer 3 hash'

primer3 = {}
while line = gets do
  key, value = line.split(/=/, 2)
  primer3[key.downcase.to_sym] = value.chomp
end

puts primer3
于 2013-06-15T11:33:48.220 に答える
-1

わかりました（ほとんど）持っています。唯一の問題は、各値の末尾に \n を追加することです。

puts 'Primer 3 hash'

primer3 = {}
while line = gets do
  key, value = line.split(/\=/)
  puts key
  puts value
  primer3[key.downcase] = value
end

puts primer3

{"sequence_id"=>"example\n",  "sequence_template"=>"GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG\n", "sequence_target"=>"37,21\n", "primer_task"=>"pick_detection_primers\n", "primer_pick_left_primer"=>"1\n", "primer_pick_internal_oligo"=>"1\n", "primer_pick_right_primer"=>"1\n", "primer_opt_size"=>"18\n", "primer_min_size"=>"15\n", "primer_max_size"=>"21\n", "primer_max_ns_accepted"=>"1\n", "primer_product_size_range"=>"75-100\n", "p3_file_flag"=>"1\n", "sequence_internal_excluded_region"=>"37,21\n", "primer_explain_flag"=>"1\n", "primer_thermodynamic_parameters_path"=>"/usr/local/Cellar/primer3/2.3.4/bin/primer3_config/\n", "primer_left_explain"=>"considered 65, too many Ns 17, low tm 48, ok 0\n", "primer_right_explain"=>"considered 228, low tm 159, high tm 12, high hairpin stability 22, ok 35\n", "primer_internal_explain"=>"considered 0, ok 0\n", "primer_pair_explain"=>"considered 0, ok 0\n", "primer_left_num_returned"=>"0\n", "primer_right_num_returned"=>"0\n", "primer_internal_num_returned"=>"0\n", "primer_pair_num_returned"=>"0\n", ""=>"\n"}
于 2013-06-15T11:32:16.880 に答える