==错误==分析YAML文件时捕获异常

Question

我似乎无法找出我的yaml文件有什么问题。我复制了这个例子，并在10个不同的迭代中填写了我的样本，试图找出问题所在，我似乎能让它工作

    orientation: "fr",
    type: "paired-end",
    right reads: [
      "/users/drob2727/supercomputer/Bon1read1.fastq",
      "/users/drob2727/supercomputer/Bon2read1.fastq",
      "/users/drob2727/supercomputer/Bon3read1.fastq"

    ],
    left reads: [
      "/users/drob2727/supercomputer/Bon1read2.fastq",
      "/users/drob2727/supercomputer/Bon2read2.fastq",
      "/users/drob2727/supercomputer/Bon3read2.fastq"

    ]

我得到了类似的错误

== Error ==  exception caught while parsing YAML file (/wheeler/scratch/drob2727/matreads8.yaml):
while parsing a block mapping
  in "/wheeler/scratch/drob2727/matreads8.yaml", line 1, column 5
expected <block end>, but found ','
  in "/wheeler/scratch/drob2727/matreads8.yaml", line 16, column 6

我缩短了我的文件以便于管理，但这些都是我遇到的错误类型

Answer 1

使用我得到的另一个解析器

expected <block end>, but found ','

但在任何情况下，我的错误都在line 1, column 18。您提供的错误与粘贴的数据不匹配

从映射中删除尾部的,对我来说很好：

orientation: "fr"
type: "paired-end"
right reads: [
  "/users/drob2727/supercomputer/Bon1read1.fastq",
  "/users/drob2727/supercomputer/Bon2read1.fastq",
  "/users/drob2727/supercomputer/Bon3read1.fastq"

]
left reads: [
  "/users/drob2727/supercomputer/Bon1read2.fastq",
  "/users/drob2727/supercomputer/Bon2read2.fastq",
  "/users/drob2727/supercomputer/Bon3read2.fastq"

]

Answer 2

YAML不使用逗号。还有字典（hashmaps或JSON对象）和列表（或数组）的特定语法

你可以find an overview here。
和a good validator here

这对我很有用：

orientation: "fr"
type: "paired-end"
right reads: 
  - "/users/drob2727/supercomputer/Bon1read1.fastq"
  - "/users/drob2727/supercomputer/Bon2read1.fastq"
  - "/users/drob2727/supercomputer/Bon3read1.fastq"
left reads:
  - "/users/drob2727/supercomputer/Bon1read2.fastq"
  - "/users/drob2727/supercomputer/Bon2read2.fastq"
  - "/users/drob2727/supercomputer/Bon3read2.fastq"