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Merge v1a, support commented BEDs
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‎.github/workflows/test.yml

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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest]
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python-version: ["3.10", "3.11"]
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python-version: ["3.11"]
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name: Python ${{ matrix.python-version }} (${{ matrix.os }})
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steps:
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- uses: actions/checkout@v3
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install pytest
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python -m pip install .
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git clone https://github.com/pha4ge/primer-schemes.git
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python -m pip install '.[dev]'
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- name: Test with pytest
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env:
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PRIMASCHEMA_ROOT_PATH: ${{ github.workspace }}
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run: |
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pytest
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env:
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PRIMER_SCHEMES_PATH: "${{ github.workspace }}/primer-schemes"

‎.pre-commit-config.yaml

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.2.0
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hooks:
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- id: check-yaml
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- id: end-of-file-fixer
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- id: trailing-whitespace
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- repo: https://github.com/psf/black
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rev: 22.3.0
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hooks:
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- id: black
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.4.4
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hooks:
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- id: ruff
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args: [ --fix ]
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- id: ruff-format

‎README.md

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# Primaschema
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The toolkit for validating and building tiling amplicon PCR primer scheme definitions for inclusion in the [PHA4GE primer-schemes repository](https://github.com/pha4ge/primer-schemes), using 6 or 7 column Primal Scheme-like BED files and scheme metadata contained in a YAML file.
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**🚨 Migration to v1 scheme specification in progress**
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A toolkit for fetching, validating and interrogating tiled amplicon PCR primer scheme definitions. Provides convenient programmatic accesss to the [PHA4GE primer-schemes repository](https://github.com/pha4ge/primer-schemes), a community repository of tiled amplicons primer schemes.
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## Install (Python 3.10+)
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## Install (Python 3.8+)
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```
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```shell
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# Latest stable release
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pip install primaschema
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# Development
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git clone https://github.com/pha4ge/primaschema.git
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cd primaschema
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pip install --editable ./
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pip install --editable '.[dev]'
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pre-commit install
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pytest
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```
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Some Primaschema commands use components from the [primer-schemes](https://github.com/pha4ge/primer-schemes) repository. To show Primaschema where to find these, create the environment variable `PRIMER_SCHEMES_PATH` pointing to the location of the primer-schemes directory on your machine:
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```
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```shell
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git clone https://github.com/pha4ge/primer-schemes.git
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export PRIMER_SCHEMES_PATH="/path/to/primer-schemes"
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```
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## Usage
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```
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% primaschema --help
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% primaschema -h
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usage: primaschema [-h] [--version]
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{hash-ref,hash-bed,validate,validate-recursive,build,build-recursive,build-manifest,diff,6to7,7to6,show-non-ref-alts}
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...
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{validate,build,build-manifest,hash-ref,hash-bed,diff,6to7,7to6,plot,show-intervals,show-discordant-primers,subset,sync} ...
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positional arguments:
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{hash-ref,hash-bed,validate,validate-recursive,build,build-recursive,build-manifest,diff,6to7,7to6,show-non-ref-alts}
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{validate,build,build-manifest,hash-ref,hash-bed,diff,6to7,7to6,plot,show-intervals,show-discordant-primers,subset,sync}
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validate Validate one or more primer scheme definitions comprising info.yml, primer.bed and reference.fasta
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build Build one or more primer scheme definitions comprising info.yml, primer.bed and reference.fasta
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build-manifest Build a complete manifest of schemes contained in the specified directory
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hash-ref Generate reference sequence checksum
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hash-bed Generate a bed file checksum
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validate Validate a primer scheme bundle containing info.yml, primer.bed and reference.fasta
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validate-recursive Recursively validate primer scheme bundles in the specified directory
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build Build a primer scheme bundle containing info.yml, primer.bed and reference.fasta
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build-recursive Recursively build primer scheme bundles in the specified directory
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build-manifest Build a complete manifest of schemes contained in the specified directory
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diff Show the symmetric difference of records in two bed files
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6to7 Convert a 6 column scheme.bed file to a 7 column primer.bed file using a reference sequence
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7to6 Convert a 7 column primer.bed file to a 6 column scheme.bed file by droppign a column
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show-non-ref-alts Show primer records with sequences not matching the reference sequence
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6to7 Convert a 6 column scheme.bed file to a 7 column primer.bed file using reference backfill
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7to6 Convert a 7 column primer.bed file to a 6 column scheme.bed file by removing a column
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plot Plot amplicon and primer coords from 7 column primer.bed
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show-intervals Show amplicon start and end coordinates given a BED file of primer coordinates
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show-discordant-primers
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Show primer records with sequences not matching the reference sequence
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subset Extract a primer.bed and reference.fasta scheme subset for a single chromosome
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sync Retrieve/update local copy of remote primer scheme repository
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options:
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-h, --help show this help message and exit
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--version show program's version number and exit
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% primaschema build test/data/primer-schemes/eden/v1
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INFO: Scheme bed file has the expected number of columns (6)
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INFO: Writing info.yml with checksums
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INFO: Generating primer.bed from scheme.bed and reference.fasta
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```

‎pyproject.toml

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[build-system]
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requires = [
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"setuptools >= 64",
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"wheel >= 0.37.1",
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]
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build-backend = "setuptools.build_meta"
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requires = ["flit_core >=3.2,<4"]
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build-backend = "flit_core.buildapi"
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[project]
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name = "primaschema"
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description = "A toolkit for primer scheme defintions"
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authors = [
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{name = "Bede Constantinides", email="[email protected]"},
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{name = "Peter van Heusden", email="[email protected]"}
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]
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dynamic = ["version", "description"]
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readme = "README.md"
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requires-python = ">=3.10"
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requires-python = ">=3.8"
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keywords = ["genomics"]
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license = {text = "MIT License"}
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classifiers = [
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"Framework :: Django",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.12",
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"Environment :: Console",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: MIT License",
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"Operating System :: MacOS",
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]
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dependencies = [
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"biopython == 1.80",
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"defopt == 6.4.0",
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"pandas >= 1.5.3",
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"pre-commit",
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"pytest",
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"altair>=5.3.0",
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"biopython>=1.80",
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"defopt==6.4.0",
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"httpx>=0.27.0",
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"jsonschema",
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"pyyaml",
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"linkml==1.5.2",
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"linkml",
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"natsort>=8.4.0",
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"pandas>=1.5.3",
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"platformdirs>=4.2.2",
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"pydantic>=2.0.0",
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"pyyaml>=6.0.2",
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"vl-convert-python>=1.6.0"
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]
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dynamic = ["version"]
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[project.scripts]
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primaschema = "primaschema.cli:main"
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[tool.setuptools.dynamic]
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version = {attr = "primaschema.__version__"}
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[project.urls]
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Home = "https://github.com/pha4ge/primaschema"
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[project.optional-dependencies]
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dev = [
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"pytest",
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"pre-commit",
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"flit"
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]
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[tool.flit.external-data]
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directory = "test"
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[tool.setuptools.packages.find]
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where = ["src"]

‎src/primaschema/__init__.py

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"""Infrastructure for tiled amplicon PCR primer scheme definitions"""
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import logging
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import logging.config
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import os
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from pathlib import Path
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__version__ = "0.2.0"
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from platformdirs import user_data_dir
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__version__ = "1.0.0a0"
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SCHEMES_ARCHIVE_URL = os.environ.get(
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"PRIMASCHEMA_SCHEMES_ARCHIVE_URL",
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"https://github.com/pha4ge/primer-schemes/archive/refs/heads/main.tar.gz",
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)
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CACHE_DIR = Path(
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os.environ.get("PRIMASCHEMA_CACHE_DIR") or user_data_dir("primaschema", "PHA4GE")
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)
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PKG_DIR = Path(
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os.environ.get(
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"PRIMASCHEMA_ROOT_PATH", Path(__file__).absolute().parent.parent.parent
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)
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)
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SCHEMA_DIR = PKG_DIR / "src" / "primaschema" / "schema"
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MANIFEST_SCHEMA_PATH = SCHEMA_DIR / "manifest.json"
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MANIFEST_HEADER_PATH = SCHEMA_DIR / "manifest-header.yml"
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logging_config = {
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"version": 1,
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"disable_existing_loggers": False,
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"formatters": {
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"default": {
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"format": "%(name)s %(levelname)s: %(message)s",
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},
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},
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"handlers": {
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"console": {
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"class": "logging.StreamHandler",
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"formatter": "default",
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"level": "INFO",
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"stream": "ext://sys.stderr",
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},
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},
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"root": {
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"handlers": ["console"],
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"level": "INFO",
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},
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"loggers": {
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"primaschema": {
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"handlers": ["console"],
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"level": "INFO",
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"propagate": False,
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},
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},
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}
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logging.config.dictConfig(logging_config)
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logger = logging.getLogger("primaschema")
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# pkg_dir = Path(__file__)
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# data_dir = pkg_dir.parent / "data"
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logger.debug(f"{PKG_DIR=} {SCHEMA_DIR=}")

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