生信编程直播第12题：json格式数据的格式化

json数据大家统一用我给的测试数据，自己在浏览器打开下载：http://biotrainee.com/jbrowse/JBrowse-1.12.1/sample_data/json/modencode/modencodeMetaData.json

范例如下：

[AppleScript] 纯文本查看复制代码

{
   "types" : {
      "data set" : {
         "pluralLabel" : "data sets"
      }
   },
   "items" : [
      {
         "technique" : "ChIP-chip",
         "factor" : "BEAF-32",
         "target" : "Non TF Chromatin binding factor",
         "principal_investigator" : "White, K.",
         "Tracks" : [
            "fly/White_INSULATORS_WIG/BEAF32"
         ],
         "submission" : "21",
         "label" : "BEAF-32;Embryos 0-12 hr;ChIP-chip",
         "category" : "Other chromatin binding sites",
         "type" : "data set",
         "Developmental-Stage" : "Embryos 0-12 hr",
         "organism" : "D. melanogaster"
      },
      {
         "technique" : "ChIP-chip",
         "factor" : "CP190",
         "target" : "Non TF Chromatin binding factor",
         "principal_investigator" : "White, K.",
         "Tracks" : [
            "fly/White_INSULATORS_WIG/CP190"
         ],
         "submission" : "22",
         "label" : "CP190;Embryos 0-12 hr;ChIP-chip",
         "category" : "Other chromatin binding sites",
         "type" : "data set",
         "Developmental-Stage" : "Embryos 0-12 hr",
         "organism" : "D. melanogaster"
      },

因为帖子长度有限，我就只截取了一部分，请自己下载查看，如果是完整的json，可以用在线工具查看结构：http://json.parser.online.fr/ 如果不懂json格式的，请自行搜索哈，现在TCGA在GDC的metadata信息，就是json格式的。我们需要从这个json文件里面提取：technique factor target principal_investigator submission label category type Developmental-Stage organism key 这几列信息，当然，是可以用正则表达式做的。完成之后应该是：http://biotrainee.com/jbrowse/JBrowse-1.12.1/sample_data/json/modencode/modencodeMetaData.csv 同样可以在浏览器打开并且下载用excel查看哈

我就不多做介绍了，主要难点在于理解json，本次作业，推荐大家用已有的包，正则表达式虽然可以做，但是太麻烦了~ 给一个perl代码如下； [Perl] 纯文本查看复制代码

#!/usr/bin/env perl
use strict;
use warnings;
use autodie ':all';
use 5.10.0;
 
use JSON 2;
 
my $data = from_json( do { local $/; open my $f, '<', $ARGV[0]; scalar <$f> } );
 
my @fields = qw( technique factor target principal_investigator submission label category type Developmental-Stage organism key );
 
say join ',', map ""$_"", @fields;
 
for my $item ( @{$data->{items}} ) {
    $item->{key} = $item->{label};
    no warnings 'uninitialized';
    for my $track ( @{$item->{Tracks}} ) {
        $item->{label} = $track;
        say join ',', map ""$_"", @{$item}{@fields};
    }
}