我正在运行一个名为Primer 3的命令行程序.它接受一个输入文件并将数据返回到标准输出.我正在尝试编写一个接受该输入的
Ruby脚本,并将这些条目放入哈希.
返回的结果如下.我想在’=’符号上拆分数据,这样就可以这样:
{:SEQUENCE_ID => "example",:SEQUENCE_TEMPLATE => "GTAGTCAGTAGACNAT..etc",:SEQUENCE_TARGET => "37,21" etc }
我还想小写密钥,即:
{:sequence_id => "example",:sequence_template => "GTAGTCAGTAGACNAT..etc",:sequence_target => "37,21" etc }
这是我目前的脚本:
#!/usr/bin/ruby puts 'Primer 3 hash' primer3 = {} while line = gets do name,height = line.split(/\=/) primer3[name] = height.to_i end puts primer3
它正在归还:
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}
数据源
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
解决方法
#!/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
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