hlaont 0.1.0__tar.gz

hlaont-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Aleix Canalda
+
+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.

hlaont-0.1.0/MANIFEST.in

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+prune tests
+prune .debug
+prune src/hlaont/resources/templates/raw
+prune src/hlaont/resources/templates/pool
+prune src/hlaont/resources/anchors/build_staging
+exclude CLAUDE.md DESIGN.md ipd_audit.py ipd_audit_v3.65.0.txt
+global-exclude test_*.py __pycache__ *.py[cod]

hlaont-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: hlaont
+Version: 0.1.0
+Summary: Confidence-aware full-field HLA typing from ONT R10 long reads
+Author: Aleix Canalda
+License-Expression: MIT AND GPL-3.0-only
+Project-URL: Homepage, https://github.com/aleixcanalda/hlaont
+Project-URL: Repository, https://github.com/aleixcanalda/hlaont
+Project-URL: Issues, https://github.com/aleixcanalda/hlaont/issues
+Keywords: HLA,HLA typing,nanopore,ONT,long reads,MHC,bioinformatics,genomics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: src/hlaont/resources/anchors/vendor/FUFIHLA_LICENSE
+License-File: src/hlaont/resources/models/vendor/BADREAD_LICENSE
+Requires-Dist: pysam
+Requires-Dist: numpy
+Requires-Dist: pyyaml
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: types-PyYAML; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Dynamic: license-file
+
+# hlaont
+
+Confidence-aware, full-field HLA typing from Oxford Nanopore (ONT) R10 long reads, designed for population-scale sequencing.
+
+Hlaont does the following:
+
+- Types **41 HLA/MIC/TAP genes**.
+- Estimates **copy number per gene** rather than assuming diploidy at every locus.
+- Reports **C4A/C4B total copy number and long/short-form composition** (the complement C4 segmental duplication).
+- Flags **novel alleles** (`novel:intronic`, `novel:utr`, `novel:synonymous`, `novel:nonsynonymous`, `novel:null`, `extension`).
+- Accepts **FASTQ or BAM/CRAM** input, and can use real read-backed phase (`HP`/`PS` tags) when available.
+
+## Requirements
+
+- Python ≥ 3.11
+- [`minimap2`](https://github.com/lh3/minimap2) and [`samtools`](https://github.com/samtools/samtools) on `PATH` (external CLI tools, not pip-installable — install via conda/bioconda: `conda install -c bioconda minimap2 samtools`)
+
+## Installation
+
+```bash
+# from source
+git clone https://github.com/aleixcanalda/hlaont.git
+cd hlaont
+pip install -e .
+
+# or, once published:
+# pip install hlaont
+# conda install -c bioconda hlaont
+```
+
+### First-time setup
+
+The package ships the anchor set, models and a pre-extracted assembly bundle, but the template pool is built from IPD-IMGT/HLA once before `hlaont run` will work:
+
+```bash
+hlaont update-db --db-dir hlaont_db/   # downloads IPD-IMGT/HLA and builds the pool into hlaont_db/
+hlaont run SAMPLE_ID reads.fastq --db-dir hlaont_db/ --out-dir OUT/
+```
+
+`--db-dir` can also be set once with `export HLAONT_DB=hlaont_db/`; without either, the pool lives inside the installed package.
+
+`hlaont update-anchors --db-dir hlaont_db/` rebuilds the anchor set against a new pool (maintainers only; needs `cd-hit-est` on PATH).
+
+## Usage
+
+```bash
+# FASTQ input
+hlaont run SAMPLE_ID reads.fastq --out-dir OUT/
+
+# BAM/CRAM input (region set auto-derived from the @SQ header — no build/reference flag needed)
+hlaont run SAMPLE_ID --bam aligned.bam --out-dir OUT/
+hlaont run SAMPLE_ID --bam aligned.cram --reference ref.fa --out-dir OUT/
+
+# Use real read-backed phase (HP/PS tags), when the input BAM has them
+hlaont run SAMPLE_ID --bam phased.bam --phased --out-dir OUT/
+```
+
+Each run writes, into `--out-dir`:
+
+| file | contents |
+|---|---|
+| `{sample}.calls.tsv` | one row per haplotype call: gene, copy number, nearest allele, novelty tag, per-field GQ, read support, consensus QV |
+| `{sample}.consensus.fa` + `.consensus.qv.tsv` | the polished per-haplotype consensus sequence and its per-base quality |
+| `{sample}.variants.vcf` | variants relative to the nearest catalogued allele |
+| `{sample}.qc.json` | per-gene copy-number estimates, C4 form breakdown, phasing routing (if `--phased`), and failure reasons for any gene that couldn't be called |
+
+Run `hlaont run --help`, `hlaont update-db --help`, or `hlaont update-anchors --help` for the full flag list.
+
+## License
+
+hlaont's own code is MIT — see [LICENSE](LICENSE). The distributed package also contains Badread's error model (GPL-3.0-only), so the package as a whole is `MIT AND GPL-3.0-only`.
+
+`resources/anchors/vendor/` ports a 136-allele anchor set from [FuFiHLA](https://github.com/jingqing-hu/FuFiHLA) (MIT); `resources/models/vendor/` ports an ONT R10.4.1 error model from [Badread](https://github.com/rrwick/Badread) (GPLv3). See each `NOTICE.md`/license file for full attribution. If you use hlaont, please also cite FuFiHLA (`10.1093/bioinformatics/btag231`).

hlaont-0.1.0/README.md

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+# hlaont
+
+Confidence-aware, full-field HLA typing from Oxford Nanopore (ONT) R10 long reads, designed for population-scale sequencing.
+
+Hlaont does the following:
+
+- Types **41 HLA/MIC/TAP genes**.
+- Estimates **copy number per gene** rather than assuming diploidy at every locus.
+- Reports **C4A/C4B total copy number and long/short-form composition** (the complement C4 segmental duplication).
+- Flags **novel alleles** (`novel:intronic`, `novel:utr`, `novel:synonymous`, `novel:nonsynonymous`, `novel:null`, `extension`).
+- Accepts **FASTQ or BAM/CRAM** input, and can use real read-backed phase (`HP`/`PS` tags) when available.
+
+## Requirements
+
+- Python ≥ 3.11
+- [`minimap2`](https://github.com/lh3/minimap2) and [`samtools`](https://github.com/samtools/samtools) on `PATH` (external CLI tools, not pip-installable — install via conda/bioconda: `conda install -c bioconda minimap2 samtools`)
+
+## Installation
+
+```bash
+# from source
+git clone https://github.com/aleixcanalda/hlaont.git
+cd hlaont
+pip install -e .
+
+# or, once published:
+# pip install hlaont
+# conda install -c bioconda hlaont
+```
+
+### First-time setup
+
+The package ships the anchor set, models and a pre-extracted assembly bundle, but the template pool is built from IPD-IMGT/HLA once before `hlaont run` will work:
+
+```bash
+hlaont update-db --db-dir hlaont_db/   # downloads IPD-IMGT/HLA and builds the pool into hlaont_db/
+hlaont run SAMPLE_ID reads.fastq --db-dir hlaont_db/ --out-dir OUT/
+```
+
+`--db-dir` can also be set once with `export HLAONT_DB=hlaont_db/`; without either, the pool lives inside the installed package.
+
+`hlaont update-anchors --db-dir hlaont_db/` rebuilds the anchor set against a new pool (maintainers only; needs `cd-hit-est` on PATH).
+
+## Usage
+
+```bash
+# FASTQ input
+hlaont run SAMPLE_ID reads.fastq --out-dir OUT/
+
+# BAM/CRAM input (region set auto-derived from the @SQ header — no build/reference flag needed)
+hlaont run SAMPLE_ID --bam aligned.bam --out-dir OUT/
+hlaont run SAMPLE_ID --bam aligned.cram --reference ref.fa --out-dir OUT/
+
+# Use real read-backed phase (HP/PS tags), when the input BAM has them
+hlaont run SAMPLE_ID --bam phased.bam --phased --out-dir OUT/
+```
+
+Each run writes, into `--out-dir`:
+
+| file | contents |
+|---|---|
+| `{sample}.calls.tsv` | one row per haplotype call: gene, copy number, nearest allele, novelty tag, per-field GQ, read support, consensus QV |
+| `{sample}.consensus.fa` + `.consensus.qv.tsv` | the polished per-haplotype consensus sequence and its per-base quality |
+| `{sample}.variants.vcf` | variants relative to the nearest catalogued allele |
+| `{sample}.qc.json` | per-gene copy-number estimates, C4 form breakdown, phasing routing (if `--phased`), and failure reasons for any gene that couldn't be called |
+
+Run `hlaont run --help`, `hlaont update-db --help`, or `hlaont update-anchors --help` for the full flag list.
+
+## License
+
+hlaont's own code is MIT — see [LICENSE](LICENSE). The distributed package also contains Badread's error model (GPL-3.0-only), so the package as a whole is `MIT AND GPL-3.0-only`.
+
+`resources/anchors/vendor/` ports a 136-allele anchor set from [FuFiHLA](https://github.com/jingqing-hu/FuFiHLA) (MIT); `resources/models/vendor/` ports an ONT R10.4.1 error model from [Badread](https://github.com/rrwick/Badread) (GPLv3). See each `NOTICE.md`/license file for full attribution. If you use hlaont, please also cite FuFiHLA (`10.1093/bioinformatics/btag231`).

hlaont-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=77", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "hlaont"
+version = "0.1.0"
+description = "Confidence-aware full-field HLA typing from ONT R10 long reads"
+readme = "README.md"
+# hlaont's own code is MIT; resources/models/vendor/nanopore2023.gz is
+# Badread's error model, GPL-3.0-only (see that directory's NOTICE.md).
+license = "MIT AND GPL-3.0-only"
+license-files = [
+    "LICENSE",
+    "src/hlaont/resources/anchors/vendor/FUFIHLA_LICENSE",
+    "src/hlaont/resources/models/vendor/BADREAD_LICENSE",
+]
+authors = [{ name = "Aleix Canalda" }]
+requires-python = ">=3.11"
+dependencies = [
+    "pysam",
+    "numpy",
+    "pyyaml",
+]
+keywords = ["HLA", "HLA typing", "nanopore", "ONT", "long reads", "MHC", "bioinformatics", "genomics"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+[project.optional-dependencies]
+dev = ["pytest", "ruff", "mypy", "types-PyYAML", "build", "twine"]
+
+[project.urls]
+Homepage = "https://github.com/aleixcanalda/hlaont"
+Repository = "https://github.com/aleixcanalda/hlaont"
+Issues = "https://github.com/aleixcanalda/hlaont/issues"
+
+[project.scripts]
+hlaont = "hlaont.cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["hlaont*"]
+
+# Checked-in resources only; templates/raw, templates/pool and
+# anchors/build_staging are regenerated by update-db/update-anchors.
+[tool.setuptools.package-data]
+hlaont = [
+    "resources/genes.yaml",
+    "resources/models/*.yaml",
+    "resources/models/vendor/*",
+    "resources/regions/*.bed",
+    "resources/regions/*.yaml",
+    "resources/anchors/*.gz",
+    "resources/anchors/*.json",
+    "resources/anchors/vendor/*",
+    "resources/templates/assembly_bundle/*",
+    "resources/controls/*.gz",
+]
+
+[tool.setuptools.exclude-package-data]
+"*" = ["test_*.py", "*.pyc"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]

hlaont-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

hlaont-0.1.0/src/hlaont/__init__.py

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+__version__ = "0.1.0"