python - 使用 bash 脚本处理 JSON

Question

我正在编写一个执行一些操作的 bash 脚本。现在它将一些文件复制到正确的目录中并运行一些命令。我需要这个 bash 脚本来编辑 JSON 文件。本质上，此脚本会将一段 JSON 附加到 file.JSON 中存在的现有 JSON 对象。我不能只追加数据，因为 JSON 片段必须是现有 JSON 对象的一部分(应该添加到 tracks 数组)。那么这可能与 bash 脚本有关吗？我应该只编写另一个 python 或 R 脚本来处理这个 JSON 逻辑，还是有更优雅的解决方案。谢谢你的帮助。

file.JSON looks like this...
    {
       "formatVersion" : 1,
       "tracks" : [
          {
             "key" : "Reference sequence",
             "chunkSize" : 20000,
             "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
             "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
             "type" : "SequenceTrack",
             "seqType" : "dna",
             "category" : "Reference sequence",
             "label" : "DNA"
          },
          {
             "type" : "FeatureTrack",
             "label" : "gff_track1",
             "trackType" : null,
             "key" : "gff_track1",
             "compress" : 0,
             "style" : {
                "className" : "feature"
             },
             "storeClass" : "JBrowse/Store/SeqFeature/NCList",
             "urlTemplate" : "tracks/gff_track1/{refseq}/trackData.json"
          },
          {
             "storeClass" : "JBrowse/Store/SeqFeature/NCList",
             "style" : {
                "className" : "feature"
             },
             "urlTemplate" : "tracks/ITAG2.4_gene_models.gff3/{refseq}/trackData.json",
             "key" : "ITAG2.4_gene_models.gff3",
             "compress" : 0,
             "trackType" : null,
             "label" : "ITAG242.4_gene_models.gff3",
             "type" : "FeatureTrack"
          },
          {
             "urlTemplate" : "g-231FRL.bam",
             "storeClass" : "JBrowse/Store/SeqFeature/BAM",
             "label" : "g-1FRL.bam",
             "type" : "JBrowse/View/Track/Alignments2",
             "key" : "g-1FRL.bam"
          }
       ]
    }

the JSON snippet looks like this ...

      {
         "urlTemplate": "AX2_filtered.vcf.gz",
         "label": "AX2_filtered.vcf.gz",
         "storeClass": "JBrowse/Store/SeqFeature/VCFTabix", 
         "type": "CanvasVariants"
      }

Answer 1

帮自己一个忙，安装jq ，那么就很简单了:

jq -n 'input | .tracks += [inputs]' file.json snippet.json > out.json

如果没有合适的解析器，尝试修改结构化数据(如 JSON)是徒劳的，jq 确实让这一切变得简单。

但是，如果您更喜欢通过 Python 来完成它(尽管对于这种任务来说它有点矫枉过正)，它与使用 jq 一样直接:

import json

with open("file.json", "r") as f, open("snippet.json", "r") as s, open("out.json", "w") as u:
    data = json.load(f)  # parse `file.json`
    data["tracks"].append(json.load(s))  # parse `snippet.json` and append it to `.tracks[]`
    json.dump(data, u, indent=4)  # encode the data back to JSON and write it to `out.json`