mkprobes

mkprobes is the combinatorial FISH probe-design toolkit used to build SOLAR probesets (splint/padlock, STARmap-style). It provides a CLI covering the full workflow, from a reference to an orderable oligo pool:

0. project    mkprobes init                  scaffold a project
1. dataset    mkprobes prepare | ingest      reference (mouse/human) | any species
2. targets    mkprobes chkgenes / convert-to-transcripts
3. codebook   mkprobes make-codebook
4. probes     mkprobes run-panel             candidates -> screen -> construct, all targets
5. panel QC   mkprobes filter-genes
6. assembly   mkprobes assemble              -> orderable oligos

Start with Getting started, which walks through all of it. mkprobes --help prints the same order, and every command takes --help.

Provenance

This repository was extracted from chaichontat/fishtools (commit cd91ef7, "Add standalone mkprobes package"; extracted 2026-08-20). The full pre-extraction development history remains browsable there under fishtools/mkprobes/, which is now frozen legacy — all probe-design development happens here. The MHD codebook matrices (src/mkprobes/data/mhd/) and the splint/padlock header/footer table (src/mkprobes/data/headerfooter.csv) were vendored from the same repository (static/ and data/).

Requirements

• Python ≥ 3.12
• External tools on PATH for dataset preparation and screening: Bowtie 2, Jellyfish, and (for final panel assembly) RepeatMasker. All are available via bioconda.

Installation

With uv (external tools must already be on PATH):

uv sync --extra dev
source .venv/bin/activate
mkprobes --help

Or with conda/mamba — one environment containing the package and the external tools (bowtie2, jellyfish, gffread) from bioconda:

mamba env create -f environment.yml
conda activate mkprobes
mkprobes --help

See the installation docs for details.

Tests

With the environment activated:

pip install -e ".[dev]"
pytest

Notes

• The experimental picker and readouts notebooks from the legacy package are excluded (import-time side effects, stale dependencies).
• Project-specific panel generation and assembly drivers are retained under scripts/. They are distributed in the source archive, not installed as console commands. scripts/generate_mhd_matrices.py is the (scratch) generator for the vendored MHD matrices.