aiva-agent 0.2.1__tar.gz

aiva_agent-0.2.1/LICENSE

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aiva_agent-0.2.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: aiva-agent
+Version: 0.2.1
+Summary: Clinical-genomics agent: ask natural-language questions over a local VCF and get annotated, literature-grounded answers.
+Author-email: Tarun Mamidi <tarun@mamidi.ai>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/MHSPL/aiva-agent
+Project-URL: Repository, https://github.com/MHSPL/aiva-agent
+Project-URL: Issues, https://github.com/MHSPL/aiva-agent/issues
+Keywords: genomics,vcf,variant-classification,acmg,bioinformatics,clinical-genomics
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: openai-agents==0.14.8
+Requires-Dist: openai==2.33.0
+Requires-Dist: duckdb==1.5.2
+Requires-Dist: httpx==0.28.1
+Requires-Dist: requests==2.33.1
+Requires-Dist: myvariant==1.0.0
+Requires-Dist: ddgs==9.14.1
+Requires-Dist: trafilatura==2.0.0
+Requires-Dist: python-dotenv==1.2.2
+Provides-Extra: dev
+Requires-Dist: pytest==9.0.3; extra == "dev"
+Requires-Dist: pytest-asyncio==1.3.0; extra == "dev"
+Requires-Dist: respx==0.23.1; extra == "dev"
+Requires-Dist: responses==0.26.0; extra == "dev"
+Dynamic: license-file
+
+# aiva-agent
+
+A standalone CLI clinical-genomics agent. Ask natural-language questions about a local VCF, gather variant annotations, search literature, find clinical trials, prioritize genes from HPO phenotypes, and run ACMG/AMP variant classification — using **any** OpenAI-compatible provider (OpenAI, Anthropic, xAI Grok, Together, Fireworks, OpenRouter, etc.).
+
+```bash
+export LLM_MODEL=gpt-5.5
+export LLM_BASE_URL=https://api.openai.com/v1
+export LLM_API_KEY=sk-...
+aiva_agent --vcf data/test.vcf.gz \
+  --prompt "How many PASS variants on chr1?"
+```
+
+## Overview
+
+The agent runs locally over a tabix-indexed VCF and orchestrates a curated set of tools to answer questions about variants, retrieve supporting literature, surface clinical trials, prioritize candidate genes from phenotype terms, and run ACMG/AMP variant classification. Tools are exposed under the following names and can be selectively turned off via `--disable`:
+
+| Tool | What it does |
+|---|---|
+| `vcf` | Run SQL-style queries over your tabix-indexed `.vcf.gz`. INFO fields are auto-flattened into columns. |
+| `annotate` | Variant annotation with action-based routing across multiple data sources. Supports plant species. |
+| `literature` | PubMed / PMC search with gene / disease / variant / chemical entity annotations. |
+| `trials` | Clinical-trials search by condition, intervention, gene/variant, phase, recruiting status; full-detail retrieval by NCT ID. |
+| `phen2gene` | Rank candidate genes for a list of HPO phenotype terms with optional exclusion penalty. |
+| `web` | `action='search'` (web search) and `action='scrape'` (clean main-content extraction from any URL). |
+| `classify` | ACMG/AMP 2015 (germline) and AMP/ASCO/CAP 2017 (somatic) classification and returns a JSON classification. |
+
+## Prerequisites
+
+- **Python 3.11+** with `pip ≥ 24`.
+- **htslib tools** (`bgzip`, `tabix`) only needed for preparing VCFs:
+  ```bash
+  brew install htslib   # macOS
+  ```
+- **A model provider's API key** — see the Provider section below. The agent works with any OpenAI-compatible endpoint.
+
+## Install
+
+```bash
+pip install aiva-agent
+```
+
+## Quick start
+
+Prepare a tabix-indexed VCF (only needed once per file):
+
+```bash
+bgzip -k path/to/sample.vcf
+tabix -p vcf path/to/sample.vcf.gz
+```
+
+Set provider credentials:
+
+```bash
+# Example for OpenAI
+export LLM_MODEL=gpt-5.5
+export LLM_BASE_URL=https://api.openai.com/v1
+export LLM_API_KEY=sk-...
+```
+
+Ask a question:
+
+```bash
+aiva_agent --vcf path/to/sample.vcf.gz \
+  --prompt "List the first 5 PASS variants on chr1."
+```
+
+## Environment variables
+
+You can drive everything via flags or env vars. Most users put the LLM credentials in `.env` once and skip the flags on every run — copy `.env.example` to `.env` to start.
+
+| Variable | Purpose | Default |
+|---|---|---|
+| `LLM_MODEL` | Model ID for the provider (e.g. `gpt-5.5`, `claude-opus-4-7`). | — |
+| `LLM_BASE_URL` | Provider's OpenAI-compatible base URL. | — |
+| `LLM_API_KEY` | Provider API key. | — |
+| `AIVA_VCF` | Default VCF path or `alias=path,...` spec. | unset (vcf tool auto-disables) |
+| `AIVA_DISABLE` | Comma-separated tools to disable. | unset (all tools on) |
+| `AIVA_MAX_TURNS` | Max agent turns per run. | `25` |
+| `AIVA_FORCE` | Overwrite `-o` destination without passing `--force`. Accepts `1/true/yes/on`. | unset |
+| `AIVA_SESSION_ID` | Conversation session ID; persist history across runs in `~/.aiva/sessions.db`. | new UUID per run |
+
+Precedence: **CLI flag > shell export > `.env` value**. So you can override per-shell or per-run without editing the file.
+
+## Usage
+
+```
+aiva_agent [--disable <tools>] [--vcf PATH] [--prompt TEXT | --prompt-file PATH]
+           [--model ID] [--base-url URL] [--api-key KEY]
+           [-o OUTPUT] [--force] [--session-id ID]
+```
+
+### `--disable`
+
+All tools are ON by default. Pass `--disable a,b` to drop tools from the agent's palette.
+
+```bash
+aiva_agent --disable vcf --model gpt-5.5 \
+  --prompt "Annotate rs113488022 and find recent papers."
+
+# Multi-tool disable: comma-separated, no spaces
+aiva_agent --disable phen2gene,web,trials --vcf data/test.vcf.gz --model gpt-5.5 \
+  --prompt "Classify the most pathogenic chr1 variant."
+```
+
+`--disable` falls back to the `AIVA_DISABLE` env var (e.g. `AIVA_DISABLE=vcf` in `.env`). The flag, when given, replaces (rather than merges with) the env value.
+
+### VCF path resolution
+
+The `vcf` tool needs a path. Provide it via `--vcf PATH` or the `AIVA_VCF` env var (set in `.env`); the flag wins if both are set. If neither is set, the `vcf` tool auto-disables itself with a one-line stderr warning and the rest of the palette runs as normal. If a path is provided but the file doesn't exist, the CLI exits with an error — that case clearly signals user intent and shouldn't be silently swallowed. Pass `--disable vcf` to skip the resolution dance entirely.
+
+#### Multiple VCFs (trio / tumor-normal)
+
+The `--vcf` flag accepts a comma-separated `alias=path` list. Each entry becomes a separately named view; the agent JOINs them at query time on `(CHROM, POS, REF)`.
+
+```bash
+aiva_agent --vcf "proband=trio/proband.vcf.gz,father=trio/father.vcf.gz,mother=trio/mother.vcf.gz" \
+  --prompt "Count de novo het variants in the proband (parents both 0/0)."
+```
+
+`AIVA_VCF` accepts the same syntax (`AIVA_VCF=proband=p.vcf.gz,father=f.vcf.gz` in `.env`).
+
+**Prefer a multisample VCF when you have one.** If you've run joint calling and produced a single multisample file, pass it as one VCF. Joint-called VCFs use explicit `./.` for missing genotypes; an outer-JOIN across separate per-sample files turns those into NULL, which the agent has to defensively `coalesce(..., './.')` to read correctly. For trio analyses the joint-called single-file path is genomically more correct.
+
+### Three ways to pass a prompt
+
+```bash
+# 1. Inline
+aiva_agent --vcf data/test.vcf.gz --prompt "How many variants on chr1?"
+
+# 2. From a file (UTF-8, trailing whitespace stripped)
+aiva_agent --vcf data/test.vcf.gz --prompt-file prompts/chr1_audit.txt
+
+# 3. From stdin (Unix pipe)
+echo "How many variants on chr2?" | aiva_agent --vcf data/test.vcf.gz --prompt -
+```
+
+### Writing the answer to a file
+
+```bash
+# Convenience flag — creates parent dirs, refuses to clobber unless --force
+aiva_agent --model gpt-5.5 --disable vcf \
+  --prompt "..." -o reports/answer.md
+
+# Or shell redirection (warnings go to stderr)
+aiva_agent --model gpt-5.5 --disable vcf \
+  --prompt "..." > answer.md
+```
+
+### Provider configuration
+
+The agent uses **any OpenAI-compatible endpoint**. You provide three pieces of information:
+
+| Argument | Purpose | Env var fallback |
+|---|---|---|
+| `--model` | Model ID exactly as the provider expects | `LLM_MODEL` |
+| `--base-url` | Provider's base URL | `LLM_BASE_URL` |
+| `--api-key` | Provider's API key | `LLM_API_KEY` |
+
+#### Common provider URLs
+
+```bash
+# OpenAI
+aiva_agent --model gpt-5.5 --base-url https://api.openai.com/v1 --api-key sk-... ...
+
+# Anthropic (uses their OpenAI-compatible endpoint)
+aiva_agent --model claude-opus-4-7 --base-url https://api.anthropic.com/v1 --api-key sk-ant-... ...
+
+# xAI Grok
+aiva_agent --model grok-2 --base-url https://api.x.ai/v1 --api-key xai-... ...
+
+# OpenRouter (catch-all multi-provider service)
+aiva_agent --model anthropic/claude-opus-4-7 --base-url https://openrouter.ai/api/v1 --api-key sk-or-... ...
+```
+
+For repeated use against one provider, set env vars once and skip all three flags. Two equivalent ways:
+
+```bash
+# A. Shell exports (process-scoped)
+export LLM_MODEL=gpt-5.5
+export LLM_BASE_URL=https://api.openai.com/v1
+export LLM_API_KEY=sk-...
+aiva_agent --disable vcf --prompt "Annotate rs113488022"
+
+# B. .env file in your working directory (auto-loaded)
+$EDITOR .env                       # fill in LLM_MODEL / LLM_BASE_URL / LLM_API_KEY
+aiva_agent --disable vcf --prompt "Annotate rs113488022"
+```
+
+**Security note:** prefer `export LLM_API_KEY=...` over `--api-key sk-...` so the secret doesn't leak into shell history or `ps`.
+
+### Conversation sessions
+
+By default each `aiva_agent` invocation is stateless. To carry context across calls, set `--session-id` (or `AIVA_SESSION_ID`) to any string you like; history is stored in a single sqlite file at `~/.aiva/sessions.db` — no server, no setup. If you don't set one, the CLI prints an auto-generated ID on stderr that you can copy to resume:
+
+```bash
+export AIVA_SESSION_ID=case-2026-05
+aiva_agent --prompt "Patient has chr7:117559590 G>A in CFTR. Remember it."
+aiva_agent --prompt "What variant did I just mention, and what gene?"
+```
+
+Each session ID is independent — pick a fresh one per case to keep histories from bleeding into each other.
+
+### Use from a notebook or Python script
+
+Set env vars in one cell, call `aiva_agent(...)` in the next; calls within the same kernel automatically share a session, so follow-up questions remember the prior turn.
+
+```python
+# cell 1
+import os
+os.environ["LLM_API_KEY"] = "sk-..."
+os.environ["LLM_BASE_URL"] = "https://api.openai.com/v1"
+os.environ["LLM_MODEL"] = "gpt-5.5"
+os.environ["AIVA_VCF"] = "data/sample.vcf.gz"
+
+# cell 2
+from aiva_agent import aiva_agent
+print(aiva_agent("List 3 likely-pathogenic variants from vcf."))
+print(aiva_agent("Of those, which is in a recessive disease gene?"))  # remembers
+```
+
+To start a fresh conversation mid-notebook, call `reset_session()`. To pin a specific ID (e.g. resume across kernel restarts), set `AIVA_SESSION_ID` in env or pass `session_id="my-case"` to `aiva_agent`. Per-call kwargs `vcf=`, `disable=`, `model=`, `base_url=`, `api_key=` override the corresponding env vars.
+
+## Examples
+
+```bash
+# All tools are on by default — pass --disable vcf for prompts that don't need
+# a local VCF, or set AIVA_DISABLE / AIVA_VCF in .env to make it permanent.
+
+# Variant annotation
+aiva_agent --disable vcf --model gpt-5.5 \
+  --prompt "Annotate rs113488022. Report ClinVar significance and population AF."
+
+# Literature search
+aiva_agent --disable vcf --model gpt-5.5 \
+  --prompt "Find 3 recent papers on TP53 R175H in lung cancer."
+
+# Clinical trials
+aiva_agent --disable vcf --model gpt-5.5 \
+  --prompt "Find phase 2 recruiting BRAF V600E melanoma trials."
+
+# HPO -> genes
+aiva_agent --disable vcf --model gpt-5.5 \
+  --prompt "Rank candidate genes for HP:0001250 + HP:0001263."
+
+# Web search + scrape (free, no API key)
+aiva_agent --disable vcf --model gpt-5.5 \
+  --prompt "Find and scrape the latest NCCN melanoma guideline summary."
+
+# ACMG/AMP classification
+aiva_agent --disable vcf --model gpt-5.5 \
+  --prompt "Classify rs113488022 (BRAF V600E) under AMP for melanoma on GRCh38."
+
+# VCF query + literature (vcf tool turns on automatically once a path is provided)
+aiva_agent --vcf data/test.vcf.gz --model gpt-5.5 \
+  --prompt "Find any TP53 variants and pull supporting literature."
+```
+
+## License
+
+Apache-2.0. See `LICENSE`.