Add Pynteny MCP server (mcp/)#105
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Adds an MCP (Model Context Protocol) server under mcp/ that exposes the Pynteny API as 6 tools (info, validate/parse synteny structure, build, search, download) so MCP-compatible agents (Claude, DeepSeek, etc.) can drive Pynteny in natural language. Includes a no-API-key smoke test and a Claude+DeepSeek example agent. This lives in the repo but is intentionally kept out of the pynteny PyPI package (packaging includes only src/pynteny), so it does not affect the distribution. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Adds a Model Context Protocol (MCP) server under
mcp/that exposes the Pynteny API as tools, so MCP-compatible agents (Claude Desktop, Claude Code, or a custom client driving Claude / DeepSeek / etc.) can run synteny-aware HMM searches in natural language.Contents (
mcp/)src/pynteny_mcp/{server,service}.py— FastMCP server with 6 tools:get_pynteny_info,validate_synteny_structure,parse_gene_symbols,build_peptide_database,run_synteny_search,download_hmm_databases.tests/smoke_test.py— no-API-key end-to-end check against the bundled test genome (asserts the known leu-operon hits; exercisesbest_hmm_wins).examples/synteny_search_agent.py— example agent (Claude + DeepSeek).README.md,pyproject.toml,requirements.txt,.env.example,.gitignore.Not part of the PyPI package
The Pynteny distribution packages only
src/pynteny, somcp/ships in the GitHub repo but is excluded from the sdist/wheel (verified against the 1.3.0 artifacts). It's installed/run separately.🤖 Generated with Claude Code