gibsonMatt / bioneer

a tool for quickly getting the correct bcftools command

Bioneer

A bioinformatics LLM companion tool. Ask questions in your terminal (e.g., "subset 5 vcfs to 'chr1' and merge"), and immediately get a bcftools command.

bioneer uses a training set of data curated from the bcftools vx.x. manual. Related examples of valid queries and repsonses are included with the user prompt. Related examples (stored locally in a Chroma database) are chosen based on semantic similarity using embeddings generated with MiniLM-L6-v2.

Bioneer streamlines and optimizes queries by using dynamic few-shot prompt engineering to produce high quality results. The only output are "valid" bcftools commands.

Usage

bioneer ask "remove all indels from a bcf file, subset to contig '1'"

Result

bcftools view -V indels -r 1 your_file.bcf

Advanced usage

More complex operations are also possible

bioneer ask "exclude all indels, subset to contig named 'contig1', remove SNPs if more than 20 samples have missing genotypes, remove all multi-allelic sites"

Result

bcftools view -V indels,mnps,other -r contig1 -i 'F_MISSING <= 0.2' -m2 -M2 your_vcf.vcf

Configure

bioneer will automatically configure itself, with the exception of your OPENAI_APIKEY. Set this variable yourself, for example by running

export OPENAI_APIKEY="you-api-key"

Vectorstores and example datasets will be stored at ~/.bioneer/. To change where bioneer looks for example data or where the Chroma database is stored, you can optionally set the following environmental variables. Environmental variables will be preferred.

VECTORSTORE="path"
PROMPT_EXAMPLES_PATH="path"

Options

$ poetry run bioneer ask --help
Usage: bioneer ask [OPTIONS] QUERY

  ask bioneer

  Parameters:

      query (str): The query to ask the LLM

      degree (int): Number of similar prompts to include in dynamic few-shot
      injection

      force (bool): Force re-create Chroma db

  Returns:

Options:
  -d, --degree INTEGER  Number of similar prompts to include
  -f, --force           Force re-create Chroma db
  --help                Show this message and exit.

Installation and Development

bioneer uses Poetry

Install dependencies with dev requirements

poetry install --with dev # installs with isort, pytest, and black

Execute in Poetry environment

poetry run bioneer ask [query]

Hooks

pytest, black, and isort are executed as pre-commit hooks

Tests

Tests as defined in tests/

Update examples

Append examples to data/data_bcftools_view.txt