== 错误 == 解析 YAML 文件时捕获的异常

Question

我似乎无法弄清楚我的 yaml 文件有什么问题。 我复制了这个例子，并在 10 次不同的迭代中填写了我的样本，试图找出问题所在，我似乎可以让它发挥作用。

    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"

    ]

我收到类似于这些的错误

== 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使其更易于管理，但这些是我遇到的错误类型。

Answer 1

使用我得到的不同解析器

expected <block end>, but found ','

但无论如何，对我来说，错误在line 1, column 18 。 您提供的错误与您粘贴的数据不匹配。

从您的映射中删除尾随,解析对我来说很好：

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（哈希图或 JSON 对象）和列表（或数组）的特定语法。

您可以在此处找到概述。
这里是一个很好的验证器。

这对我有用：

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"