如果希望处理yaml文件的结构而不关心其内容，则不需要构造本机python对象。相反，请使用节点图：

import yaml, sys
from yaml.nodes import SequenceNode, MappingNode
from yaml.resolver import BaseResolver

input = """
elements:
  - !Element
    name: element1
    gnc_script:
      - '*fcc_cores_1'
      - '*setup'
    relationship:
      - projectx
      - projectxy
      - projectxyt
      # indirect related on
      - projectxyz1

  - !Element
    name: element2
    gnc_script:
      - '*fcc_cores_1'
    relationship:
      - projectx
      - projectxy
      - projectxyt
      # indirect related on
      - projectxyz1

  - !Element
    name: element3
    gnc_script:
      - '*fcc_cores_1'
      - '*setup'
    relationship:
      - projectx
      - projectxy
      - projectxyt
      # indirect related on
      - projectxyz1
"""

node = yaml.compose(input)

visited = set()

def output(node):
  yaml.serialize(node, sys.stdout)
  sys.stdout.write("...\n")

def visit(node):
  if node in visited: return
  if node.tag == "!Element":
    node.tag = BaseResolver.DEFAULT_MAPPING_TAG
    output(node)
  visited.add(node)
  if isinstance(node, SequenceNode):
    for child in node.value:
      visit(child)
  elif isinstance(node, MappingNode):
    for k,v in node.value:
      visit(k); visit(v)

visit(node)

这将产生：

name: element1
gnc_script:
- '*fcc_cores_1'
- '*setup'
relationship:
- projectx
- projectxy
- projectxyt
- projectxyz1
...
name: element2
gnc_script:
- '*fcc_cores_1'
relationship:
- projectx
- projectxy
- projectxyt
- projectxyz1
...
name: element3
gnc_script:
- '*fcc_cores_1'
- '*setup'
relationship:
- projectx
- projectxy
- projectxyt
- projectxyz1
...

该代码包括其输入和输出到stdout，用于演示；重写 output(node) 创建所需文件并用要处理的文件替换输入。
如您所见，输入中的注解不是输出的一部分。这是因为它们被pyyaml的解析器丢弃了。用Pyaml解决这个问题没有简单的方法；你可以试试ruamel，它试图保留评论，但我不知道它的api。