gbf2xml

Use when converting GenBank flatfiles into XML for downstream EDirect or XML-based sequence annotation workflows.

安装方式

默认使用会先检查来源的 Prompt；你也可以切换为直接命令，或下载本地副本。

用 Codex 或 Claude 帮你安装复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。

直接命令不会经过审查 Prompt；运行前请先检查来源。

npx skills add https://github.com/vimalinx/bio-agent --skill gbf2xml

命令会保持在同一行。复制前请横向滚动并检查完整内容。

想先保存到本地？可下载 SkillsMP 当前能够提供的文件。

决定是否安装前，请先阅读 SKILL.md，以及 SkillsMP 当前展示的配套文件。

文件资源管理器

2 个文件

SKILL.md

来源说明 · 只读预览

name	gbf2xml
description	Use when converting GenBank flatfiles into XML for downstream EDirect or XML-based sequence annotation workflows.
disable-model-invocation	true
user-invocable	true

Convert GenBank flatfiles into XML so they can be queried with XML tools.
Bridge annotated sequence records from flatfile form into EDirect pipelines that expect XML.
Normalize GenBank content before further extraction, transformation, or archiving.

# 1) Convert a GenBank flatfile into XML
gbf2xml < records.gbf > records.xml

# 2) Convert and inspect the resulting XML structure quickly
gbf2xml < records.gbf | sed -n '1,40p'

Start from a representative GenBank flatfile sample.
Run gbf2xml through stdin redirection or a pipe.
Check that non-empty XML is produced before processing a large dataset.
Feed the XML into xtract or other downstream tools only after that smoke test passes.

This wrapper simply runs transmute -g2x, so the companion transmute binary must be on PATH.
The installed wrapper does not provide a real --help / --version interface.
Prefer stdin/pipes over relying on undocumented positional-file behavior.
Malformed flatfiles can yield empty output, so inspect a small sample before batching.