abotyper-core 0.1.0__tar.gz

abotyper_core-0.1.0/.gitignore

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+__pycache__/
+*.py[cod]
+*.egg-info/
+build/
+dist/
+.venv/
+.pytest_cache/
+.ruff_cache/
+.coverage
+# local dev helpers
+.dev_*.sh
+.dev_bioconda/

abotyper_core-0.1.0/CHANGELOG.md

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+# Changelog
+
+## 0.1.0 (2026-11-12)
+
+First release. The typing logic of nf-core/abotyper (refactor branch, `bin/` scripts) as an installable package.
+
+- Modules: `panel`, `naming`, `inputs`, `phase`, `calling`, `report`, `aggregate`, `panel_to_bed`,
+  `clair2metrics`, `clair2haplotypes`, `pileup2metrics`, `predict_phenotype`, `calibrate_panel`,
+  `rename_samples`.
+- Commands `abotyper-*` for each step, plus the pipeline's script names (`abo_panel.py`,
+  `predict_abo_phenotype.py`, ...) as aliases.
+- The ABO variant panel (v2.3.0, YAML and CSV) and the ISBT coverage table ship with the package; `--panel`
+  defaults to the bundled panel.
+- `abotyper-panel --check-isbt` compares the panel with the ISBT blood group allele database
+  (blooddatabase.isbtweb.org) and lists suggested updates: new DNA changes, new, changed or retired alleles, and
+  panel rows no current allele carries. It also reads the site's EXPORT file (`--isbt-source abo.xlsx`). The
+  baseline it diffs alleles against is the bundled snapshot of ISBT release 21 (2026-11-01).
+- A monthly workflow runs the check and opens an issue when it has suggestions.
+- Golden tests: per-sample and aggregated outputs are byte-identical to the pipeline's `bin/` scripts.

abotyper_core-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Fredrick M. Mobegi
+Copyright (c) The nf-core/abotyper team
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

abotyper_core-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: abotyper-core
+Version: 0.1.0
+Summary: ABO blood group typing logic from long-read amplicon data, as used by nf-core/abotyper
+Project-URL: Homepage, https://github.com/fmobegi/abotyper-core
+Project-URL: Pipeline, https://github.com/nf-core/abotyper
+Project-URL: Publication, https://pubmed.ncbi.nlm.nih.gov/40564908/
+Author: Fredrick M. Mobegi
+License-Expression: MIT
+License-File: LICENSE
+Keywords: ABO,ISBT,bioinformatics,blood group,genotyping,nanopore
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Requires-Dist: numpy>=1.26
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: pandas>=2.2
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: xlsxwriter>=3.1
+Provides-Extra: test
+Requires-Dist: openpyxl>=3.1; extra == 'test'
+Requires-Dist: pytest>=8; extra == 'test'
+Requires-Dist: ruff>=0.14; extra == 'test'
+Description-Content-Type: text/markdown
+
+# abotyper-core
+
+A Python package to assign ABO genotypes and alleles from variant calls using the ISBT database panel.
+
+The ABO blood group typing logic from [nf-core/abotyper](https://github.com/nf-core/abotyper), packaged as a Python
+library and a set of command-line tools.
+
+It loads and validates the ABO variant panel, turns Clair3 calls and BAM pileups into per-position evidence,
+resolves phenotype, genotype and ISBT allele names, and writes the per-sample and aggregated result tables.
+
+> **Research use only.** Not validated for clinical diagnosis or transfusion decisions.
+
+## Install
+
+```bash
+pip install abotyper-core                     # PyPI
+conda install -c conda-forge -c bioconda abotyper-core   # Bioconda
+```
+
+Containers: `quay.io/biocontainers/abotyper-core` (BioContainers, built from the Bioconda package).
+
+Python 3.11 or newer. Dependencies: pandas, numpy, pyyaml, xlsxwriter and openpyxl.
+
+## Commands
+
+| Command | What it does |
+| --- | --- |
+| `abotyper-panel` | Validate and summarise a variant panel; `--check-isbt` compares it with the ISBT allele table |
+| `abotyper-panel-to-bed` | BED of panel positions for Clair3 `--bed_fn` and `bcftools view -R` |
+| `abotyper-clair2metrics` | Per-position metrics from Clair3 VCFs |
+| `abotyper-clair2haplotypes` | Phased haplotypes from Clair3 VCFs |
+| `abotyper-pileup2metrics` | Per-position metrics from BAM pileups |
+| `abotyper-predict-phenotype` | Phenotype, genotype and ISBT allele calls per sample |
+| `abotyper-aggregate` | Aggregate per-sample results into the final report (xlsx, csv) |
+| `abotyper-calibrate-panel` | Fill amplicon coordinates into a panel from a reference |
+| `abotyper-rename-samples` | Rename samples from a mapping sheet |
+
+Each command takes `--help`. Commands that read the panel default to the bundled
+`abotyper_core/data/abo_variant_panel.yaml`; pass `--panel` to use another one.
+
+### Checking the panel against ISBT
+
+```bash
+abotyper-panel --check-isbt                          # fetch the live ISBT ABO allele table
+abotyper-panel --isbt-source ABO_allele_table.xlsx   # or the file the site's EXPORT button downloads
+```
+
+The check reads the ABO alleles from the [ISBT blood group allele database](https://blooddatabase.isbtweb.org/system/ABO)
+and compares them with the panel and its coverage table (`abo_isbt_v9_coverage.tsv`, which records how the panel
+handles every ISBT DNA change). It lists suggestions; it never edits the panel:
+
+| Kind | Meaning |
+| --- | --- |
+| `new_change` | a DNA change in a current allele that neither the panel nor the coverage table knows (exon 1 changes are flagged as assay gaps) |
+| `new_allele` | an allele not in the baseline snapshot, and whether its changes are already handled |
+| `changed_allele` | an allele whose changes or phenotype differ from the baseline |
+| `retired_allele` | a baseline allele that is gone or marked obsolete |
+| `panel_change_not_in_isbt` | a panel row whose change no current allele carries |
+| `release` | the ISBT release differs from the one the panel was last checked against |
+
+Alleles are compared with a baseline snapshot, by default the bundled `isbt_abo_alleles.tsv` (ISBT release 21,
+2026-11-01). After reviewing and updating the panel, save a new baseline with `--isbt-snapshot`. Use
+`--isbt-report` to write the suggestions as a TSV and `--fail-on-changes` (exit status 3) in scheduled jobs; the
+repository's monthly `ISBT check` workflow opens an issue when there is something to review.
+
+The ISBT site has no documented allele API: the check reads the allele records the ABO page embeds, and fails
+with a clear message if the page layout changes. `--isbt-source` with an export file always works.
+
+### Legacy names
+
+The package also installs the script names the pipeline's modules call today (`abo_panel.py`, `panel_to_bed.py`,
+`clair2metrics.py`, `clair2haplotypes.py`, `pileup2metrics.py`, `predict_abo_phenotype.py`,
+`aggregate_abo_reports.py`), so the pipeline can switch from its `bin/` scripts to this package without changing
+module scripts.
+
+## Library use
+
+```python
+from abotyper_core import load_panel, default_panel_path
+
+panel = load_panel(default_panel_path())
+for marker in panel.calibrated():
+    print(marker.id, marker.resolved_position())
+```
+
+## Development
+
+```bash
+pip install -e ".[test]"
+ruff check src tests
+pytest
+```
+
+The golden tests run every step on ten fixture samples and compare the outputs byte for byte (xlsx cell by cell)
+with `tests/golden/`. After an intended output change, regenerate them with `UPDATE_GOLDEN=1 pytest` and review the
+diff. `tests/requirements-pinned.txt` lists the versions the golden files were made with.
+
+## Citation
+
+If you use this package, please cite [nf-core/abotyper](https://github.com/nf-core/abotyper) and its publication:
+[PubMed 40564908](https://pubmed.ncbi.nlm.nih.gov/40564908/).
+
+## Licence
+
+MIT. See [LICENSE](LICENSE).

abotyper_core-0.1.0/README.md

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+# abotyper-core
+
+A Python package to assign ABO genotypes and alleles from variant calls using the ISBT database panel.
+
+The ABO blood group typing logic from [nf-core/abotyper](https://github.com/nf-core/abotyper), packaged as a Python
+library and a set of command-line tools.
+
+It loads and validates the ABO variant panel, turns Clair3 calls and BAM pileups into per-position evidence,
+resolves phenotype, genotype and ISBT allele names, and writes the per-sample and aggregated result tables.
+
+> **Research use only.** Not validated for clinical diagnosis or transfusion decisions.
+
+## Install
+
+```bash
+pip install abotyper-core                     # PyPI
+conda install -c conda-forge -c bioconda abotyper-core   # Bioconda
+```
+
+Containers: `quay.io/biocontainers/abotyper-core` (BioContainers, built from the Bioconda package).
+
+Python 3.11 or newer. Dependencies: pandas, numpy, pyyaml, xlsxwriter and openpyxl.
+
+## Commands
+
+| Command | What it does |
+| --- | --- |
+| `abotyper-panel` | Validate and summarise a variant panel; `--check-isbt` compares it with the ISBT allele table |
+| `abotyper-panel-to-bed` | BED of panel positions for Clair3 `--bed_fn` and `bcftools view -R` |
+| `abotyper-clair2metrics` | Per-position metrics from Clair3 VCFs |
+| `abotyper-clair2haplotypes` | Phased haplotypes from Clair3 VCFs |
+| `abotyper-pileup2metrics` | Per-position metrics from BAM pileups |
+| `abotyper-predict-phenotype` | Phenotype, genotype and ISBT allele calls per sample |
+| `abotyper-aggregate` | Aggregate per-sample results into the final report (xlsx, csv) |
+| `abotyper-calibrate-panel` | Fill amplicon coordinates into a panel from a reference |
+| `abotyper-rename-samples` | Rename samples from a mapping sheet |
+
+Each command takes `--help`. Commands that read the panel default to the bundled
+`abotyper_core/data/abo_variant_panel.yaml`; pass `--panel` to use another one.
+
+### Checking the panel against ISBT
+
+```bash
+abotyper-panel --check-isbt                          # fetch the live ISBT ABO allele table
+abotyper-panel --isbt-source ABO_allele_table.xlsx   # or the file the site's EXPORT button downloads
+```
+
+The check reads the ABO alleles from the [ISBT blood group allele database](https://blooddatabase.isbtweb.org/system/ABO)
+and compares them with the panel and its coverage table (`abo_isbt_v9_coverage.tsv`, which records how the panel
+handles every ISBT DNA change). It lists suggestions; it never edits the panel:
+
+| Kind | Meaning |
+| --- | --- |
+| `new_change` | a DNA change in a current allele that neither the panel nor the coverage table knows (exon 1 changes are flagged as assay gaps) |
+| `new_allele` | an allele not in the baseline snapshot, and whether its changes are already handled |
+| `changed_allele` | an allele whose changes or phenotype differ from the baseline |
+| `retired_allele` | a baseline allele that is gone or marked obsolete |
+| `panel_change_not_in_isbt` | a panel row whose change no current allele carries |
+| `release` | the ISBT release differs from the one the panel was last checked against |
+
+Alleles are compared with a baseline snapshot, by default the bundled `isbt_abo_alleles.tsv` (ISBT release 21,
+2026-11-01). After reviewing and updating the panel, save a new baseline with `--isbt-snapshot`. Use
+`--isbt-report` to write the suggestions as a TSV and `--fail-on-changes` (exit status 3) in scheduled jobs; the
+repository's monthly `ISBT check` workflow opens an issue when there is something to review.
+
+The ISBT site has no documented allele API: the check reads the allele records the ABO page embeds, and fails
+with a clear message if the page layout changes. `--isbt-source` with an export file always works.
+
+### Legacy names
+
+The package also installs the script names the pipeline's modules call today (`abo_panel.py`, `panel_to_bed.py`,
+`clair2metrics.py`, `clair2haplotypes.py`, `pileup2metrics.py`, `predict_abo_phenotype.py`,
+`aggregate_abo_reports.py`), so the pipeline can switch from its `bin/` scripts to this package without changing
+module scripts.
+
+## Library use
+
+```python
+from abotyper_core import load_panel, default_panel_path
+
+panel = load_panel(default_panel_path())
+for marker in panel.calibrated():
+    print(marker.id, marker.resolved_position())
+```
+
+## Development
+
+```bash
+pip install -e ".[test]"
+ruff check src tests
+pytest
+```
+
+The golden tests run every step on ten fixture samples and compare the outputs byte for byte (xlsx cell by cell)
+with `tests/golden/`. After an intended output change, regenerate them with `UPDATE_GOLDEN=1 pytest` and review the
+diff. `tests/requirements-pinned.txt` lists the versions the golden files were made with.
+
+## Citation
+
+If you use this package, please cite [nf-core/abotyper](https://github.com/nf-core/abotyper) and its publication:
+[PubMed 40564908](https://pubmed.ncbi.nlm.nih.gov/40564908/).
+
+## Licence
+
+MIT. See [LICENSE](LICENSE).

abotyper_core-0.1.0/pyproject.toml

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+[build-system]
+requires = ["hatchling>=1.25"]
+build-backend = "hatchling.build"
+
+[project]
+name = "abotyper-core"
+dynamic = ["version"]
+description = "ABO blood group typing logic from long-read amplicon data, as used by nf-core/abotyper"
+readme = "README.md"
+license = "MIT"
+license-files = ["LICENSE"]
+requires-python = ">=3.11"
+authors = [{ name = "Fredrick M. Mobegi" }]
+keywords = ["ABO", "blood group", "genotyping", "ISBT", "nanopore", "bioinformatics"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "pandas>=2.2",
+    "numpy>=1.26",
+    "pyyaml>=6.0",
+    "xlsxwriter>=3.1",
+    "openpyxl>=3.1",
+]
+
+[project.optional-dependencies]
+test = ["pytest>=8", "openpyxl>=3.1", "ruff>=0.14"]
+
+[project.urls]
+Homepage = "https://github.com/fmobegi/abotyper-core"
+Pipeline = "https://github.com/nf-core/abotyper"
+Publication = "https://pubmed.ncbi.nlm.nih.gov/40564908/"
+
+[project.scripts]
+# one command per pipeline step
+abotyper-panel = "abotyper_core.panel:main"
+abotyper-panel-to-bed = "abotyper_core.panel_to_bed:main"
+abotyper-clair2metrics = "abotyper_core.clair2metrics:main"
+abotyper-clair2haplotypes = "abotyper_core.clair2haplotypes:main"
+abotyper-pileup2metrics = "abotyper_core.pileup2metrics:main"
+abotyper-predict-phenotype = "abotyper_core.predict_phenotype:main"
+abotyper-aggregate = "abotyper_core.aggregate:main"
+abotyper-calibrate-panel = "abotyper_core.calibrate_panel:main"
+abotyper-rename-samples = "abotyper_core.rename_samples:main"
+# the script names nf-core/abotyper calls today, so its modules can switch to the package unchanged
+"abo_panel.py" = "abotyper_core.panel:main"
+"panel_to_bed.py" = "abotyper_core.panel_to_bed:main"
+"clair2metrics.py" = "abotyper_core.clair2metrics:main"
+"clair2haplotypes.py" = "abotyper_core.clair2haplotypes:main"
+"pileup2metrics.py" = "abotyper_core.pileup2metrics:main"
+"predict_abo_phenotype.py" = "abotyper_core.predict_phenotype:main"
+"aggregate_abo_reports.py" = "abotyper_core.aggregate:main"
+
+[tool.hatch.version]
+path = "src/abotyper_core/__init__.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/abotyper_core"]
+
+[tool.hatch.build.targets.sdist]
+include = ["src/abotyper_core", "tests", "README.md", "LICENSE", "CHANGELOG.md"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+[tool.ruff]
+target-version = "py311"
+line-length = 140
+
+[tool.ruff.lint]
+select = ["E4", "E7", "E9", "F", "B006", "B008", "B904"]

abotyper_core-0.1.0/src/abotyper_core/__init__.py

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+"""abotyper-core: ABO blood group typing logic from long-read amplicon data.
+
+The panel-driven typing used by nf-core/abotyper: loading and validating the ABO variant panel, turning Clair3 and
+BAM-pileup evidence into per-position calls, resolving phenotype, genotype and ISBT allele names, and writing the
+result tables. Each step is also a command-line tool (see the README).
+
+Research use only; not validated for clinical diagnosis.
+"""
+
+__version__ = "0.1.0"
+
+from .panel import Panel, PanelError, VariantMarker, default_panel_path, load_panel  # noqa: E402
+
+__all__ = ["Panel", "PanelError", "VariantMarker", "default_panel_path", "load_panel", "__version__"]