From 475ecf13719ec299f5ea09bdabb2ac467cb57094 Mon Sep 17 00:00:00 2001 From: Conrad Date: Fri, 23 Oct 2026 17:36:12 -0400 Subject: [PATCH 1/3] build: Stand up the package skeleton, packaging and shared test fixtures Somewhere for the ported data path to land. No logic yet, so that a later failure is attributable to the port rather than to the scaffolding it lands on. Follows abdenlab/giql, the nearest sibling and quadrat's own dependency: src layout, hatchling, ruff at line-length 89, four-space indentation, PEP 735 dependency groups. Python floor is 3.11 rather than cherimoya's 3.10, because polars-bio, polars and giql are all gated there and the pileup is not an optional part of what this package is for. Runtime dependencies shear from cherimoya's sixteen to six, with the pileup engine behind a `pileup` extra. Every one of those imports is already lazy inside a function body upstream, so a caller that streams windows over tables it already has never pays for them. Two defects in cherimoya's manifest are corrected rather than carried: pyfaidx is imported by production code but declared only in a dev group, and cherimoya.workers is missing from the explicit package list, so it never ships in a built distribution. Hatchling's src discovery makes the second unrepeatable. The ruff select is pinned rather than left to the default. Ruff 0.17 enables UP, SIM, FURB and RUF by default, and UP032 alone fires on cherimoya's `str.format` style throughout -- so the default would demand a style migration inside the change that moves the code, which is the one thing that makes a port unreviewable. giql resolves from the public commit at the tip of its cherimoya-mvp branch. The datafusion-bio target is not on PyPI and cherimoya pins a path outside its own tree, which a published package cannot inherit. That commit's library code is identical to what cherimoya builds against; the only delta is benchmark material outside src. The fixture layer is the substantive half. Cherimoya has no data-path fixtures in conftest -- every one is module-local, and the FASTA, BAM and BED quintet is duplicated five ways differing only in chromosome sizes and window geometry. Porting that duplication would multiply it, so the builders take the geometry as arguments and the five sets collapse onto one factory. Cut-site builders arrive with the writer they need, in the pileup slice. The cache directory is pointed at a fresh temporary directory at import time, before anything imports the package, because default_cache_dir reads it per call: set later, the first reader would still see the user's own cache, and a surviving entry would satisfy a test written to exercise a cold build. --- .github/workflows/test.yml | 50 + .gitignore | 33 + MANIFEST.in | 7 + README.md | 24 + pyproject.toml | 108 ++ src/quadrat/__init__.py | 41 + tests/__init__.py | 0 tests/_builders.py | 169 ++ tests/conftest.py | 129 ++ tests/test_builders.py | 357 +++++ uv.lock | 3112 ++++++++++++++++++++++++++++++++++++ 11 files changed, 4030 insertions(+) create mode 100644 .github/workflows/test.yml create mode 100644 .gitignore create mode 100644 MANIFEST.in create mode 100644 README.md create mode 100644 pyproject.toml create mode 100644 src/quadrat/__init__.py create mode 100644 tests/__init__.py create mode 100644 tests/_builders.py create mode 100644 tests/conftest.py create mode 100644 tests/test_builders.py create mode 100644 uv.lock diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..b440812 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,50 @@ +name: Run tests + +on: + pull_request: + branches: + - main + push: + branches: + - main + +permissions: {} + +concurrency: + group: ${{ github.workflow }}-${{ github.head_ref || github.ref }} + cancel-in-progress: true + +jobs: + test: + name: Python ${{ matrix.python-version }} + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: + - '3.11' + - '3.12' + steps: + - name: Checkout code + uses: actions/checkout@v4 + with: + persist-credentials: false + + - name: Install uv + uses: astral-sh/setup-uv@v5 + with: + python-version: ${{ matrix.python-version }} + + # The pileup extra resolves giql from a git revision, so the + # checkout needs network here. See the comment on + # `[tool.uv.sources]` in pyproject.toml. + - name: Install + run: uv sync --all-extras --group dev + + - name: Lint + run: | + uv run ruff format --check src tests + uv run ruff check src tests + + - name: Test + run: uv run pytest -q diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..89d14e2 --- /dev/null +++ b/.gitignore @@ -0,0 +1,33 @@ +# macOS +.DS_Store + +# Python +__pycache__/ +*.py[cod] +*$py.class +*.so +build/ +dist/ +sdist/ +wheels/ +*.egg-info/ +*.egg +.eggs/ + +# Environments +.venv/ +venv/ + +# Tooling +.pytest_cache/ +.ruff_cache/ +.hypothesis/ +.coverage +coverage.xml +htmlcov/ + +# Docs +docs/_build/ + +# Jupyter +.ipynb_checkpoints/ diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..0ad3c41 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,7 @@ +# The whole test tree, so the tests run from an sdist exactly as they do +# from the repository -- without conftest.py they would run against a +# different cache directory than the one the suite assumes. +graft tests + +global-exclude */.ipynb_checkpoints/* +global-exclude *.py[cod] diff --git a/README.md b/README.md new file mode 100644 index 0000000..142da20 --- /dev/null +++ b/README.md @@ -0,0 +1,24 @@ +# quadrat + +Sequence-to-function training data, straight from BAM. + +A quadrat is the fixed-size frame a field ecologist drops on the ground to tally everything inside it, moved across a landscape by a sampling design chosen separately from the frame. This package is that: a fixed-length window, placed at loci by a sampling scheme, tallying the cut sites that fall inside. + +Everything between a set of alignments and a batch of `(sequence, signal)` pairs is independent of the model that consumes them. `quadrat` implements that span — the pileup, the window cache, the sampler and the loader — so any sequence-to-function architecture can be trained without reimplementing it. + +## Status + +Under construction. The data path is being extracted from [cherimoya](https://github.com/conradbzura/cherimoya); see [#1](https://github.com/abdenlab/quadrat/issues/1) for the specification and the slices it lands in. + +## Install + +```bash +pip install quadrat # stream windows over cut-site tables +pip install "quadrat[pileup]" # also build those tables from alignments +``` + +The pileup reads alignments through [polars-bio](https://github.com/biodatageeks/polars-bio) and transpiles its aggregate with [giql](https://github.com/abdenlab/giql). Both are imported only when a pileup runs, so the base install stays light for a caller who already has tables. + +## License + +MIT. diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..6fb01cd --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,108 @@ +[build-system] +build-backend = "hatchling.build" +requires = ["hatchling"] + +[project] +authors = [ + { name = "Nezar Abdennur", email = "nabdennur@gmail.com" }, + { name = "Conrad Bzura", email = "conradbzura@gmail.com" }, +] +classifiers = [ + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Programming Language :: Python :: 3", + "Topic :: Scientific/Engineering :: Bio-Informatics", +] +description = "Sequence-to-function training data, straight from BAM." +dynamic = ["version"] +license = "MIT" +maintainers = [ + { name = "Nezar Abdennur", email = "nabdennur@gmail.com" }, + { name = "Conrad Bzura", email = "conradbzura@gmail.com" }, +] +name = "quadrat" +readme = "README.md" +requires-python = ">=3.11" + +# Floors, not tested ceilings. 3.11 rather than 3.10 because the pileup +# engine -- polars-bio, polars, giql -- is gated there, and the pileup is +# not an optional part of what this package is for. +dependencies = [ + "numpy>=1.14.2", + "pandas>=1.3.3", + "torch>=2.9.0", + "tqdm>=4.64.1", + "joblib>=1.0.0", + "tangermeme>=1.5.0", +] + +# The pileup reads alignments through polars-bio's BAM provider and +# transpiles its aggregate with giql. Every one of these is imported +# lazily inside a function body, so a caller that only streams windows +# over cut-site tables it already has never pays for them. +# +# `pyfaidx` belongs here rather than in a dev group: `chrom_lengths` and +# `SequenceStore` import it at runtime. +[project.optional-dependencies] +pileup = [ + "polars-bio>=0.35.1", + "polars>=1.30", + "giql", + "pyfaidx", +] + +[dependency-groups] +dev = [ + "pytest>=9.1.1", + "pytest-mock>=3.14", + "hypothesis>=6.0.0", + "pysam", + "pybigtools", + "pyBigWig", + "ruff>=0.1.0", +] +docs = [ + "sphinx>=7.0", + "sphinx-autobuild>=2024.0", + "sphinx-book-theme>=1.1", + "sphinx-design>=0.6", +] + +# BRANCH-ONLY. The datafusion-bio GIQL target is not on PyPI and lives on +# a proof-of-concept branch, so this pins the public commit at that +# branch's tip. Its library code is identical to what cherimoya builds +# against; the only delta is benchmark material outside `src`. Replace +# with a version specifier once the target reaches `main` and ships. +[tool.uv.sources] +giql = { git = "https://github.com/abdenlab/giql", rev = "59c74276e07cc4680cb24303a9192c3a71c11d59" } + +[tool.hatch.version] +path = "src/quadrat/__init__.py" + +[tool.hatch.build.targets.wheel] +packages = ["src/quadrat"] + +[tool.ruff] +line-length = 89 + +# Stated explicitly rather than left to the default, which has widened +# over ruff releases and would otherwise change what passes when the +# pin moves. Pyflakes plus the pycodestyle errors that are errors: +# undefined names, unused imports, broken syntax. +# +# Deliberately absent are the style-migration families -- UP, SIM, FURB, +# RUF. The code ported from cherimoya uses `str.format` throughout and +# `class X(object)` by convention. Flagging either would mean rewriting +# thousands of lines in the same change that moves them, which is the +# one thing that makes a port unreviewable. +[tool.ruff.lint] +select = ["E4", "E7", "E9", "F"] + +[tool.ruff.format] +docstring-code-format = true + +[tool.pytest.ini_options] +markers = [ + "integration: exercises a real cross-boundary interaction rather than a unit", +] +filterwarnings = ["ignore::DeprecationWarning"] diff --git a/src/quadrat/__init__.py b/src/quadrat/__init__.py new file mode 100644 index 0000000..1c3f44e --- /dev/null +++ b/src/quadrat/__init__.py @@ -0,0 +1,41 @@ +"""Training data for sequence-to-function models, from alignments. + +A sequence-to-function model consumes pairs of a one-hot DNA sequence +over an input window and a measured signal profile over a shorter, +concentric output window. Everything between a set of alignments and a +batch of such pairs is independent of the architecture downstream, and +that is what this package implements. + +Four terms, used consistently throughout: + +``locus`` + A genomic coordinate, typically a peak summit or a sampled + background position. + +``window`` + A fixed-length interval centred on a locus, in two nested lengths -- + an input window supplying sequence and a shorter output window + supplying signal. + +``channel`` + One measured track. + +``cut-site table`` + The intermediate representation: a per-contig, position-sorted + Parquet table of ``(position, value)`` pairs for one channel, + written once by the pileup and read many times by the loader. + +``draw`` + One ``(locus, jitter offset, strand)`` triple the sampler emits, so + a locus yields many draws under jitter and reverse-complement + augmentation. + +The pileup reads alignments through polars-bio and transpiles its +aggregate with giql, both of which are installed by the ``pileup`` +extra and imported only when a pileup actually runs. A caller that +already has cut-site tables needs neither. +""" + +__version__ = "0.1.0.dev0" + +__all__ = ["__version__"] diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/_builders.py b/tests/_builders.py new file mode 100644 index 0000000..88eb28a --- /dev/null +++ b/tests/_builders.py @@ -0,0 +1,169 @@ +"""Synthetic genomics inputs for the test suite. + +Not a ``test_`` module, so pytest does not collect it. Everything here +is a plain function taking an output path, because the fixtures that +wrap them differ only in geometry -- chromosome sizes, window lengths, +how many reads -- and a parameterised builder is the one thing five +near-identical fixture sets can collapse onto. + +``pysam`` is imported lazily. A test module that needs none of the BAM +builders should not be skipped for want of it. +""" + +import gzip +import os +import random + + +def write_fasta( + path, chrom_sizes, *, seed=0, soft_mask=(), n_runs=(), index=False, line_width=60 +): + """Write a random FASTA over ``chrom_sizes`` and return its path. + + ``soft_mask`` and ``n_runs`` are iterables of ``(chrom, start, + stop)`` half-open intervals, lowercased and replaced with ``N`` + respectively. Both exist because masking is a property the sequence + reader has to handle rather than an accident of real references. + + ``index`` writes a ``.fai`` beside the file. It needs pysam, so it + is off by default -- only the stores actually read through an index. + """ + + rng = random.Random(seed) + sequences = {} + for chrom, size in chrom_sizes.items(): + sequences[chrom] = [rng.choice("ACGT") for _ in range(size)] + + for chrom, start, stop in soft_mask: + bases = sequences[chrom] + bases[start:stop] = [base.lower() for base in bases[start:stop]] + for chrom, start, stop in n_runs: + sequences[chrom][start:stop] = ["N"] * (stop - start) + + with open(path, "w") as handle: + for chrom, size in chrom_sizes.items(): + handle.write(">{}\n".format(chrom)) + bases = "".join(sequences[chrom]) + for offset in range(0, size, line_width): + handle.write(bases[offset : offset + line_width] + "\n") + + if index: + import pysam + + pysam.faidx(path) + return path + + +def alignment_header(chrom_sizes): + """A coordinate-sorted header over ``chrom_sizes``. + + Pass a contig the reference does not have to exercise the + header-against-reference refusal; nothing here objects to it. + """ + + import pysam + + return pysam.AlignmentHeader.from_dict( + { + "HD": {"VN": "1.6", "SO": "coordinate"}, + "SQ": [{"SN": chrom, "LN": size} for chrom, size in chrom_sizes.items()], + } + ) + + +def aligned_read(header, name, chrom, pos, cigar="20M", flag=0, mapq=30): + """One aligned segment with a dummy query and qualities. + + ``chrom=None`` builds an unplaced record, which is the shape the + pileup has to drop rather than mis-locate. Query length follows the + CIGAR so soft clips and deletions stay self-consistent. + """ + + import pysam + + read = pysam.AlignedSegment(header) + read.query_name = name + read.flag = flag + if chrom is None: + read.reference_id = -1 + read.reference_start = -1 + else: + read.reference_id = header.get_tid(chrom) + read.reference_start = pos + read.cigarstring = cigar + + length = read.infer_query_length() or 20 + read.query_sequence = "A" * length + read.query_qualities = pysam.qualitystring_to_array("I" * length) + read.mapping_quality = mapq + return read + + +def write_bam(path, reads, header): + """Sort ``reads`` into ``path``, index it, and return the path. + + Written unsorted and then sorted rather than sorted in memory, + because the index is what makes a contig predicate a region query + and a BAM whose order disagrees with its index is a failure mode + worth being unable to produce by accident. + """ + + import pysam + + staging = path + ".unsorted.bam" + with pysam.AlignmentFile(staging, "wb", header=header) as out: + for read in reads: + out.write(read) + pysam.sort("-o", path, staging) + pysam.index(path) + os.remove(staging) + return path + + +def write_random_bam(path, header, chrom_sizes, *, n_reads=40, seed=0, read_length=20): + """A BAM of ``n_reads`` randomly placed records, half on each strand. + + Reads land on the first contig twice as often as the others, so a + contig batch split is not uniform and a per-contig count is not the + same number everywhere. + """ + + rng = random.Random(seed) + chroms = list(chrom_sizes) + reads = [] + for index in range(n_reads): + chrom = chroms[0] if index % 3 else chroms[index % len(chroms)] + span = chrom_sizes[chrom] - read_length * 2 + reads.append( + aligned_read( + header, + "r{}".format(index), + chrom, + rng.randrange(0, max(1, span)), + cigar="{}M".format(read_length), + flag=16 if index % 2 else 0, + ) + ) + return write_bam(path, reads, header) + + +def write_bed(path, rows): + """Write ``(chrom, start, stop)`` rows, gzipped when ``path`` says so. + + Exclusion lists are conventionally gzipped and locus files + conventionally are not, and both readers have to cope, so the + suffix decides rather than a flag. + """ + + opener = gzip.open if str(path).endswith(".gz") else open + with opener(path, "wt") as handle: + for row in rows: + chrom, start, stop = row[:3] + handle.write("{}\t{}\t{}\n".format(chrom, start, stop)) + return path + + +def intervals(chrom, start, stop, step, width): + """``(chrom, start, stop)`` rows every ``step`` bases over a range.""" + + return [(chrom, pos, pos + width) for pos in range(start, stop, step)] diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..2f39fc9 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,129 @@ +"""Suite-wide setup and the one fixture every data-path module wants. + +The environment block runs at import time, before anything imports +``quadrat``, because ``default_cache_dir`` reads its variable per call +rather than once -- so setting it later would leave the first reader +pointed at the real user cache. +""" + +import os +import tempfile + +import pytest + +from tests import _builders + +# Progress bars in a captured suite are noise that also slows it down. +os.environ.setdefault("TQDM_DISABLE", "1") + +# A fresh cache per session, and never the user's own. Two reasons, and +# the second is the one that bites: writing to `~/.cache` pollutes a +# real install, and a surviving entry from an earlier run would satisfy +# a test written to exercise a cold build, which then passes while +# testing nothing. +os.environ.setdefault( + "QUADRAT_CACHE_DIR", + tempfile.mkdtemp(prefix="quadrat-test-cache-"), +) + + +class Corpus(object): + """Paths to one synthetic genome and whatever was built over it. + + A plain attribute bag rather than a dict so a typo is an + ``AttributeError`` at the point of use. + """ + + __slots__ = ( + "root", + "chrom_sizes", + "fasta", + "bams", + "peaks", + "negatives", + "exclusion", + ) + + def __init__(self, root, chrom_sizes): + self.root = root + self.chrom_sizes = chrom_sizes + self.fasta = None + self.bams = [] + self.peaks = None + self.negatives = None + self.exclusion = None + + def path(self, name): + """A path inside this corpus's directory, as a string.""" + + return str(self.root / name) + + +@pytest.fixture(scope="session") +def corpus_factory(tmp_path_factory): + """Build a synthetic corpus to a given geometry. + + Session-scoped because building one costs a sort and an index per + BAM, and the five geometries the suite needs are fixed. Each call + gets its own directory, so two corpora never share a file even when + their chromosome sizes agree. + + Signature mirrors what the modules that used to carry their own + copies of this actually varied: the chromosome sizes, how many + reads, where the loci sit, and whether the sequence is masked. + """ + + def build( + name, + chrom_sizes, + *, + n_bams=0, + n_reads=40, + seed=0, + index_fasta=False, + soft_mask=(), + n_runs=(), + header_contigs=None, + peaks=(), + negatives=(), + exclusion=(), + ): + root = tmp_path_factory.mktemp(name) + corpus = Corpus(root, chrom_sizes) + corpus.fasta = _builders.write_fasta( + corpus.path("genome.fa"), + chrom_sizes, + seed=seed, + soft_mask=soft_mask, + n_runs=n_runs, + index=index_fasta, + ) + + if n_bams: + # `header_contigs` may name a contig the reference lacks, + # which is the asymmetry the header refusal exists to catch. + header = _builders.alignment_header(header_contigs or chrom_sizes) + corpus.bams = [ + _builders.write_random_bam( + corpus.path("s{}.bam".format(index)), + header, + chrom_sizes, + n_reads=n_reads, + seed=seed + index, + ) + for index in range(n_bams) + ] + + if peaks: + corpus.peaks = _builders.write_bed(corpus.path("peaks.bed"), peaks) + if negatives: + corpus.negatives = _builders.write_bed( + corpus.path("negatives.bed"), negatives + ) + if exclusion: + corpus.exclusion = _builders.write_bed( + corpus.path("exclusion.bed.gz"), exclusion + ) + return corpus + + return build diff --git a/tests/test_builders.py b/tests/test_builders.py new file mode 100644 index 0000000..4fa503a --- /dev/null +++ b/tests/test_builders.py @@ -0,0 +1,357 @@ +"""Tests for the synthetic-input builders the suite is built on. + +These are new tests rather than ported ones, so they follow the project +test conventions -- BDD names, Given-When-Then docstrings, Arrange-Act- +Assert phases. The ported suites keep cherimoya's style until a separate +change converts them. + +The builders are test infrastructure, which is exactly why they are +tested: every later assertion about the pileup or the window cache is +an assertion about data these functions produced, so a builder that +silently writes the wrong thing makes the suite agree with itself and +with nothing else. +""" + +import gzip +import os + +import pytest + +from tests import _builders + +pysam = pytest.importorskip("pysam") + +CHROM_SIZES = {"chr1": 1000, "chr2": 500} + + +def test_write_fasta_should_write_every_contig_at_its_declared_length(tmp_path): + """Test that the FASTA holds exactly the requested bases. + + Given: + A mapping of two contig names to lengths. + When: + write_fasta renders it. + Then: + It should write each contig at its declared length over the + DNA alphabet. + """ + + # Arrange + path = str(tmp_path / "genome.fa") + + # Act + _builders.write_fasta(path, CHROM_SIZES) + + # Assert + sequences = {} + name = None + with open(path) as handle: + for line in handle: + if line.startswith(">"): + name = line[1:].strip() + sequences[name] = "" + else: + sequences[name] += line.strip() + assert {k: len(v) for k, v in sequences.items()} == CHROM_SIZES + assert set("".join(sequences.values())) <= set("ACGT") + + +def test_write_fasta_should_mask_the_intervals_it_is_given(tmp_path): + """Test that soft masking and N runs land where they were asked for. + + Given: + A soft-masked interval and an N run, each on a known contig. + When: + write_fasta renders it. + Then: + It should lowercase the first interval and fill the second with + N, leaving the surrounding bases uppercase ACGT. + """ + + # Arrange + path = str(tmp_path / "masked.fa") + + # Act + _builders.write_fasta( + path, CHROM_SIZES, soft_mask=[("chr1", 100, 120)], n_runs=[("chr1", 200, 210)] + ) + + # Assert + bases = "" + with open(path) as handle: + for line in handle: + if line.startswith(">chr2"): + break + if not line.startswith(">"): + bases += line.strip() + assert bases[100:120] == bases[100:120].lower() + assert bases[200:210] == "N" * 10 + assert bases[120:200] == bases[120:200].upper() + + +def test_write_fasta_should_be_reproducible_from_its_seed(tmp_path): + """Test that the same seed yields the same sequence. + + Given: + Two renders of one geometry, one seed shared and one differing. + When: + The files are compared. + Then: + It should produce identical bases for the shared seed and + different bases otherwise. + """ + + # Arrange + first = str(tmp_path / "a.fa") + second = str(tmp_path / "b.fa") + third = str(tmp_path / "c.fa") + + # Act + _builders.write_fasta(first, CHROM_SIZES, seed=7) + _builders.write_fasta(second, CHROM_SIZES, seed=7) + _builders.write_fasta(third, CHROM_SIZES, seed=8) + + # Assert + with open(first) as a, open(second) as b, open(third) as c: + first_bases, second_bases, third_bases = a.read(), b.read(), c.read() + assert first_bases == second_bases + assert first_bases != third_bases + + +def test_write_bam_should_write_a_sorted_indexed_file(tmp_path): + """Test that reads handed over out of order come back sorted. + + Given: + Three reads supplied in descending coordinate order. + When: + write_bam writes them. + Then: + It should emit them in ascending coordinate order beside an + index. + """ + + # Arrange + header = _builders.alignment_header(CHROM_SIZES) + reads = [ + _builders.aligned_read(header, "r{}".format(i), "chr1", pos) + for i, pos in enumerate((400, 200, 100)) + ] + path = str(tmp_path / "reads.bam") + + # Act + _builders.write_bam(path, reads, header) + + # Assert + assert os.path.exists(path + ".bai") + with pysam.AlignmentFile(path, "rb") as bam: + starts = [read.reference_start for read in bam.fetch()] + assert starts == sorted(starts) + + +def test_aligned_read_should_size_the_query_from_the_cigar(tmp_path): + """Test that a soft-clipped CIGAR gets a query long enough for it. + + Given: + A read with five soft-clipped and fifteen matched bases. + When: + aligned_read builds it. + Then: + It should give the record a twenty-base query, so the CIGAR and + the sequence agree. + """ + + # Arrange + header = _builders.alignment_header(CHROM_SIZES) + + # Act + read = _builders.aligned_read(header, "clipped", "chr1", 300, cigar="5S15M", flag=16) + + # Assert + assert read.query_length == 20 + assert read.reference_start == 300 + assert read.is_reverse + + +def test_aligned_read_should_build_an_unplaced_record_for_a_missing_contig(): + """Test that passing no contig yields an unplaced read. + + Given: + A read whose contig is None. + When: + aligned_read builds it. + Then: + It should carry no reference and no start, which is the shape + the pileup has to drop rather than mis-locate. + """ + + # Arrange + header = _builders.alignment_header(CHROM_SIZES) + + # Act + read = _builders.aligned_read(header, "unplaced", None, None) + + # Assert + assert read.reference_id == -1 + assert read.reference_start == -1 + + +def test_write_bed_should_gzip_when_the_suffix_says_so(tmp_path): + """Test that the path suffix decides the compression. + + Given: + One row written to a .bed path and the same row to a .bed.gz. + When: + Each is read back with the matching reader. + Then: + It should produce the same tab-separated line from both. + """ + + # Arrange + rows = [("chr1", 500, 600)] + plain = str(tmp_path / "x.bed") + packed = str(tmp_path / "x.bed.gz") + + # Act + _builders.write_bed(plain, rows) + _builders.write_bed(packed, rows) + + # Assert + with open(plain) as handle: + assert handle.read() == "chr1\t500\t600\n" + with gzip.open(packed, "rt") as handle: + assert handle.read() == "chr1\t500\t600\n" + + +def test_intervals_should_step_across_the_range_at_a_fixed_width(tmp_path): + """Test that the interval helper tiles a range as asked. + + Given: + A range of 400 to 600 at a step of 75 and a width of 20. + When: + intervals builds the rows. + Then: + It should return every start in the range, each paired with a + stop one width along. + """ + + # Act + rows = _builders.intervals("chr1", 400, 600, 75, 20) + + # Assert + assert rows == [("chr1", 400, 420), ("chr1", 475, 495), ("chr1", 550, 570)] + + +def test_corpus_factory_should_build_only_what_it_was_asked_for(corpus_factory): + """Test that unrequested pieces of a corpus stay absent. + + Given: + A corpus requested with a FASTA and peaks but no negatives, + exclusion list or alignments. + When: + The factory builds it. + Then: + It should populate the FASTA and the peaks and leave the rest + unset, so a test cannot read a file it never asked to exist. + """ + + # Act + corpus = corpus_factory("minimal", CHROM_SIZES, peaks=[("chr1", 100, 140)]) + + # Assert + assert os.path.exists(corpus.fasta) + assert os.path.exists(corpus.peaks) + assert corpus.bams == [] + assert corpus.negatives is None + assert corpus.exclusion is None + + +def test_corpus_factory_should_give_each_corpus_its_own_directory(corpus_factory): + """Test that two corpora of one geometry do not share files. + + Given: + Two corpora requested with identical chromosome sizes. + When: + Both are built. + Then: + It should place them in different directories, so neither can + observe the other's writes. + """ + + # Act + first = corpus_factory("twin", CHROM_SIZES) + second = corpus_factory("twin", CHROM_SIZES) + + # Assert + assert first.root != second.root + assert first.fasta != second.fasta + + +def test_corpus_factory_should_declare_header_contigs_the_reference_lacks( + corpus_factory, +): + """Test that a BAM header may name a contig outside the reference. + + Given: + A corpus whose header contigs include one absent from the + chromosome sizes the FASTA was built from. + When: + The factory builds an alignment over it. + Then: + It should write the BAM with that contig in its header, which + is the asymmetry the header-against-reference refusal exists to + catch. + """ + + # Arrange + header_contigs = dict(CHROM_SIZES, chrZ=800) + + # Act + corpus = corpus_factory( + "asymmetric", CHROM_SIZES, n_bams=1, header_contigs=header_contigs + ) + + # Assert + with pysam.AlignmentFile(corpus.bams[0], "rb") as bam: + assert "chrZ" in set(bam.references) + assert "chrZ" not in corpus.chrom_sizes + + +def test_quadrat_should_expose_a_version(): + """Test that the package declares a version. + + Given: + A fresh install of the package. + When: + quadrat is imported. + Then: + It should expose a non-empty __version__, which the build + backend reads to version the distribution. + """ + + # Act + import quadrat + + # Assert + assert quadrat.__version__ + + +def test_conftest_should_point_the_cache_at_a_temporary_directory(): + """Test that the suite never reads or writes the user's own cache. + + Given: + A session whose conftest has been imported. + When: + The cache directory variable is read. + Then: + It should name an existing 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The review history is versioned by its own repository under .sdlc; the guides are config rather than a project artifact. --- .gitignore | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.gitignore b/.gitignore index 89d14e2..d75dc6d 100644 --- a/.gitignore +++ b/.gitignore @@ -31,3 +31,9 @@ docs/_build/ # Jupyter .ipynb_checkpoints/ + +# SDLC working state: local review roles, guides and accumulated review +# documents. Untracked here as it is in the sibling projects -- the +# review history is versioned by its own repo under .sdlc, and the +# guides are local working config rather than a project artifact. +.sdlc/ From 2b53c897bee9bd322d36d9edafc26559af289551 Mon Sep 17 00:00:00 2001 From: Conrad Date: Fri, 23 Oct 2026 17:36:13 -0400 Subject: [PATCH 3/3] feat: Port the pileup, cut-site tables and the memory planner Ports cherimoya's pileup across eight modules, split along seams that already existed in the 2,652-line module it came from. Output is byte-identical: the same two alignments through cherimoya and through quadrat produce the same Parquet, per contig, at one contig batch and at three, manifests included. The split resolves a cycle rather than imposing one. Upstream, the planner and the SQL layer import from each other inside function bodies because the module graph would not otherwise admit them. Here plan.py is a leaf, sql.py and alignments.py depend on it, run.py depends on plan, and the four lazy imports that existed to tolerate the cycle are gone -- which is the test of whether the seam was real. Three names had to change because the polars-bio session is process-global. Its table names carry a quadrat_ prefix rather than a cherimoya_ one, and the cache directory variable follows, so both packages can be imported into one process during the transition. That same globalness is why a worker runs one pileup at a time, and the reasoning travels with the names. Two things deliberately do not change. CUT_SITE_SUFFIX and MANIFEST_VERSION are cherimoya's, so a table either package writes is readable by the other; the alternative is re-piling every corpus to move between them. And `import quadrat` still pulls in none of polars, polars-bio, torch, giql or pyfaidx -- every heavy import stayed inside the function body that needs it, which is what makes the pileup extra optional rather than nominal. The wool backend is deferred rather than ported. It dispatches to workers on other machines and is the only part of the pileup needing a dependency outside this package. BACKENDS ships as serial and process, and asking for wool raises NotImplementedError naming the alternative, because a caller migrating a working configuration needs to know it is deferred and not that it never existed. Tests: 34 of cherimoya's 38 pileup tests and 8 of its 30 giql_io tests. The four dropped from each drive the cherimoya CLI. The other 18 giql_io tests cover locus loading and extraction and belong to a later slice, not here -- the earlier estimate of 26 counted tests leaving cherimoya rather than tests arriving in this module. Two ported tests needed adjusting, both for the two-backend contract rather than for the port: one asserted on an error message listing three backends, and one iterated a hardcoded tuple of them, which now reads BACKENDS so the wool backend is picked up when it lands. Also fixes a defect in the test builders from the previous commit. write_random_bam placed every read on the first contig, because the branch meant to spread them indexed the contig list by a value that was zero whenever that branch was taken. It survived review because the builder's own test only checked that reads came back sorted, so a corpus confined to one contig looked correct. The parity run found it: the pileup wrote one per-contig table where it should have written three. There is now a test asserting reads reach every contig, which is the assertion that was missing. --- pyproject.toml | 6 + src/quadrat/__init__.py | 14 +- src/quadrat/_engine.py | 121 ++++ src/quadrat/alignments.py | 259 +++++++++ src/quadrat/pileup/__init__.py | 277 ++++++++++ src/quadrat/pileup/plan.py | 382 +++++++++++++ src/quadrat/pileup/run.py | 247 +++++++++ src/quadrat/pileup/sql.py | 147 +++++ src/quadrat/reference.py | 117 ++++ src/quadrat/tables.py | 555 +++++++++++++++++++ tests/_builders.py | 7 +- tests/test_builders.py | 31 ++ tests/test_pileup.py | 972 +++++++++++++++++++++++++++++++++ tests/test_pileup_io.py | 458 ++++++++++++++++ 14 files changed, 3591 insertions(+), 2 deletions(-) create mode 100644 src/quadrat/_engine.py create mode 100644 src/quadrat/alignments.py create mode 100644 src/quadrat/pileup/__init__.py create mode 100644 src/quadrat/pileup/plan.py create mode 100644 src/quadrat/pileup/run.py create mode 100644 src/quadrat/pileup/sql.py create mode 100644 src/quadrat/reference.py create mode 100644 src/quadrat/tables.py create mode 100644 tests/test_pileup.py create mode 100644 tests/test_pileup_io.py diff --git a/pyproject.toml b/pyproject.toml index 6fb01cd..cc53b10 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -98,6 +98,12 @@ line-length = 89 [tool.ruff.lint] select = ["E4", "E7", "E9", "F"] +# A test module calls `pytest.importorskip` before importing quadrat, so +# a machine without the pileup extra skips the module instead of failing +# collection. That necessarily puts imports after statements. +[tool.ruff.lint.per-file-ignores] +"tests/*" = ["E402"] + [tool.ruff.format] docstring-code-format = true diff --git a/src/quadrat/__init__.py b/src/quadrat/__init__.py index 1c3f44e..8625f11 100644 --- a/src/quadrat/__init__.py +++ b/src/quadrat/__init__.py @@ -38,4 +38,16 @@ __version__ = "0.1.0.dev0" -__all__ = ["__version__"] +from quadrat.pileup import pileup_alignments, pileup_many +from quadrat.reference import chrom_lengths +from quadrat.tables import CUT_SITE_SUFFIX, read_manifest, require_complete + +__all__ = [ + "CUT_SITE_SUFFIX", + "__version__", + "chrom_lengths", + "pileup_alignments", + "pileup_many", + "read_manifest", + "require_complete", +] diff --git a/src/quadrat/_engine.py b/src/quadrat/_engine.py new file mode 100644 index 0000000..6aeb58e --- /dev/null +++ b/src/quadrat/_engine.py @@ -0,0 +1,121 @@ +"""The one polars-bio session, and the tables registered in it. + +polars-bio holds a single process-global session, so every table name +here carries a ``quadrat_`` prefix and nothing registers a name a +caller might also be using. The prefix is not decoration: cherimoya +registers the same shapes under ``cherimoya_``, and during the +transition both packages may be imported into one process. + +The same globalness is why a pileup worker runs one job at a time. +Two concurrent pileups would register their alignments under the same +names and read each other's reads. +""" + +import os + + +_FASTA_TABLE = "quadrat_fasta" + + +_SIZES_TABLE = "quadrat_chrom_sizes" + + +_WINDOWS_TABLE = "quadrat_windows" + + +_CUTS_TABLE = "quadrat_cuts" + + +_LOCUS_BINS_TABLE = "quadrat_locus_bins" + + +_EXCLUSION_BINS_TABLE = "quadrat_exclusion_bins" + + +_cache = { + "fasta": None, + "chrom_lengths": None, + "chrom_lengths_path": None, + "sequences": {}, + "sql": {}, +} + + +def clear_cache(): + """Forget cached chromosome lengths, sequences and transpiled queries.""" + + _cache["fasta"] = None + _cache["chrom_lengths"] = None + _cache["chrom_lengths_path"] = None + _cache["sequences"] = {} + _cache["sql"] = {} + + +### +# Engine access +### + + +def _pb(): + """Import polars-bio lazily with quiet defaults.""" + + os.environ.setdefault("TQDM_DISABLE", "1") + import polars_bio as pb + + try: + pb.set_loglevel("error") + except Exception: + pass + return pb + + +def _giql_sql(key, query, tables): + """Transpile a GIQL query for the datafusion-bio target once per process.""" + + if key not in _cache["sql"]: + from giql import transpile + + _cache["sql"][key] = transpile(query, tables=tables, dialect="datafusion-bio") + return _cache["sql"][key] + + +def _interval_tables(*specs): + from giql import Table + + return [ + Table(name, chrom_col="chrom", start_col=start, end_col=end, strand_col=None) + for name, start, end in specs + ] + + +def _register_frame(pb, name, frame): + pb.from_polars(name, frame) + + +def _explain(pb, sql): + """Return the physical plan of ``sql`` as one string.""" + + import polars + + plan = pb.sql("EXPLAIN " + sql).collect() + return ( + "\n".join( + str(v) + for col in plan.get_columns() + for v in col.to_list() + if isinstance(v, str) + ) + if isinstance(plan, polars.DataFrame) + else str(plan) + ) + + +def _sql_string(value): + """One SQL string literal, with quotes doubled. + + Contig names come from a BAM header rather than from a user, but they + are arbitrary bytes as far as the format is concerned, and a name + carrying an apostrophe would otherwise end the literal early. + """ + + return "'{}'".format(str(value).replace("'", "''")) diff --git a/src/quadrat/alignments.py b/src/quadrat/alignments.py new file mode 100644 index 0000000..735248b --- /dev/null +++ b/src/quadrat/alignments.py @@ -0,0 +1,259 @@ +"""Reading alignments: contigs, indexes, and how the genome is batched. + +A contig predicate reaches the BAM index as a region query, so a batch +costs only the records it selects rather than a full scan. That is what +makes splitting the genome nearly free, and it is why an unindexed +alignment gets a warning rather than a silent fallback -- the rows are +identical either way and only the time changes. + +The refusals here are the asymmetric half. An alignment whose header +names no contig the reference has produces an empty table rather than +an error, which is indistinguishable downstream from a genuinely empty +assay. +""" + +import collections +import gzip +import os +import struct +import warnings + +from quadrat._engine import _pb + + +# polars-bio's BAM provider returns ``start`` equal to pysam's 0-based +# ``reference_start`` and ``end`` equal to the exclusive ``reference_end`` on +# the default session, despite its docstring claiming 1-based coordinates. +# ``tests/test_giql_io.py`` pins this against pysam; bump the offset (and the +# test) if a future polars-bio release changes the convention. +_BAM_START_OFFSET = 0 + + +### +# Cut-site pileup +### + + +def register_alignments(paths, prefix="quadrat_bam"): + """Register BAM/SAM files as polars-bio tables and return their names.""" + + pb = _pb() + names = [] + for i, path in enumerate(paths): + if not path.endswith((".bam", ".sam")): + raise ValueError( + "The GIQL engine converts BAM/SAM alignments; got {}".format(path) + ) + + name = "{}_{}".format(prefix, i) + if path.endswith(".sam"): + pb.register_sam(path, name) + else: + pb.register_bam(path, name) + names.append(name) + + return names + + +def bam_contigs(path): + """Reference sequences named in a BAM header, as ``{name: length}``. + + BGZF is gzip-framed, and the header is the first thing in the file, + so this reads one block however large the alignment is -- 195 + contigs in about a millisecond on an ENCODE ATAC BAM. + + It is read directly rather than through pysam because pysam is a + development dependency, not a runtime one, and polars-bio's + ``describe_bam`` reports the column schema rather than the + reference sequences. + + Returns ``None`` for anything that is not a readable BAM -- SAM, + which is text and carries no index to restrict, but also a file + that is missing or truncated. Nothing here diagnoses: the engine + opens the same file moments later and reports it better, and a + header that cannot be read only means the pileup is not split. + """ + + if not str(path).endswith(".bam"): + return None + + try: + with gzip.open(path, "rb") as handle: + if handle.read(4) != b"BAM\x01": + return None + (length,) = struct.unpack(" best[0] and workers >= enough: + best = (workers, groups) + return best + + +def default_workers(n_jobs, backend="process", bytes_per_job=None): + """How many pileups to run at once, by default. + + One per job, bounded by the cores and by memory. The measured speed + curve flattens well before the cap (see the module docstring: 16 and + 20 workers are indistinguishable on 128 cores), so erring high costs + little speed -- what matters is not landing on the steep part, at two + or four. + + Memory is the bound that actually bites, and it bites hard: ten + pileups over 3.9 GB inputs peaked at 120 GB together. Exceeding this + budget does not make a run slow, it makes it die, so the bound is + deliberately conservative where the speed cap is not -- an envelope + over every arm measured rather than a fit through them. What the + peak is made of is :func:`projected_peak`. + + This is the worker half of :func:`plan_pileup`, which chooses the + contig batch count alongside it; the two are one decision now, since + batches are what buy the concurrency. + + Parameters + ---------- + n_jobs: int + How many pileups there are to run. + + backend: str + Accepted for symmetry with :func:`pileup_many`; the budget does + not depend on it. + + bytes_per_job: int or None + Alignment bytes one job will read. When given, the per-worker + budget scales with it, which is what makes the bound right for + small inputs as well as large. ``None`` falls back to + :data:`UNKNOWN_INPUT_PEAK_BYTES`. + """ + + if n_jobs <= 0: + return 0 + return plan_pileup(n_jobs, bytes_per_job)[0] + + +def default_partitions(workers): + """DataFusion ``target_partitions`` for one pileup among ``workers``. + + ``pileup_alignments`` otherwise sets this to every core, and the + setting is process-global, so K concurrent pileups would each ask + for the whole machine. Dividing it costs little -- one pileup gets + only about 2.1x from 14 partitions -- and avoids oversubscribing the + thread pool K-fold. + """ + + return max(1, _n_cpus() // max(1, workers)) diff --git a/src/quadrat/pileup/run.py b/src/quadrat/pileup/run.py new file mode 100644 index 0000000..e227870 --- /dev/null +++ b/src/quadrat/pileup/run.py @@ -0,0 +1,247 @@ +"""Running many pileups at once, over one of three backends. + +Concurrency is worth roughly fourfold on a large machine and nothing on +a small one, because a pileup is already internally multithreaded past +its own partition count -- one burns about two cores at a single +partition and about five at fourteen, so the machine is largely spoken +for before a second pileup starts. The curve rises steeply to about a +dozen workers and then flattens. + +The backends are verified byte-identical rather than merely +equivalent. The aggregate is an exact integer count with the scale +applied once afterwards, so there is no partition-order-dependent float +accumulation to diverge. + +A job is a plain dict of :func:`quadrat.pileup.pileup_alignments` +keyword arguments. Nothing here interprets it beyond +``target_partitions``, so it serialises by value and needs no class +definition on the far side of a process boundary. +""" + +import os + +from quadrat.pileup.plan import ( + _group_floor, + default_partitions, + plan_pileup, +) + + +#: Backends this package can dispatch to, all of them verified +#: byte-identical to each other. +BACKENDS = ("serial", "process") + +#: Backends cherimoya offers that have not been ported yet. Named +#: separately from `BACKENDS` so asking for one gets told it is +#: deferred rather than that it does not exist. +_DEFERRED_BACKENDS = ("wool",) + + +def _run_one(job, target_partitions=None, verbose=False): + """Run one pileup in this process. The unit every backend dispatches. + + Imported inside so that a worker pays for polars-bio and torch once, + when it first runs a job, rather than at module import. + """ + + from quadrat.pileup import pileup_alignments + + job = dict(job) + alignments = job.pop("alignments") + sequences = job.pop("sequences") + name = job.pop("name") + job.setdefault("verbose", verbose) + if target_partitions is not None: + job.setdefault("target_partitions", target_partitions) + return pileup_alignments(alignments, sequences, name, **job) + + +def _normalize(jobs): + # Copied, not just listed: `pileup_many` fills in defaults with + # setdefault and must not write through to the caller's dicts. + jobs = [dict(job) if isinstance(job, dict) else job for job in jobs] + for i, job in enumerate(jobs): + if not isinstance(job, dict): + raise TypeError( + "job {} must be a dict of pileup_alignments keyword " + "arguments; got {!r}".format(i, type(job).__name__) + ) + for required in ("alignments", "sequences", "name"): + if required not in job: + raise KeyError("job {} is missing {!r}".format(i, required)) + return jobs + + +def pileup_many( + jobs, + backend="serial", + workers=None, + target_partitions=None, + namespace=None, + verbose=False, +): + """Run independent cut-site pileups concurrently. + + Parameters + ---------- + jobs: list of dict + Keyword arguments for :func:`~quadrat.pileup_alignments`. + ``alignments``, ``sequences`` and ``name`` are required. Jobs must + be independent: two jobs writing the same ``name`` race, and + nothing here detects it. + + backend: str + One of :data:`BACKENDS`. + + workers: int or None + How many pileups to run at once. ``None`` uses + :func:`default_workers`. Ignored by the ``serial`` backend. + + target_partitions: int or None + Passed to each pileup, overriding what it would choose. ``None`` + uses :func:`default_partitions` for the concurrent backends and + leaves the serial backend at its whole-machine default. + + namespace: str or None + ``wool`` backend only: a LAN discovery namespace to lease workers + from, instead of (or as well as) spawning them locally. + + verbose: bool + Report progress, and pass through to each pileup. + + Returns + ------- + paths: list of list of str + Each job's written table paths, in channel order, in job order. + + Notes + ----- + Every backend returns the same paths in the same order, and the + tables they write are byte-identical; only the wall clock differs. + Exceptions propagate from the first job that raises, and the tables + of jobs that had already finished are left in place -- each one is + committed atomically on its own, so a partial run leaves complete + tables and absent ones, never a half-written table. + """ + + if backend in _DEFERRED_BACKENDS: + raise NotImplementedError( + "the {!r} backend has not been ported to quadrat yet -- see " + "https://github.com/abdenlab/quadrat/issues/1. Use " + "backend='process' to run concurrently on this " + "machine.".format(backend) + ) + if backend not in BACKENDS: + raise ValueError( + "backend must be one of {}; got {!r}".format(", ".join(BACKENDS), backend) + ) + + jobs = _normalize(jobs) + if not jobs: + return [] + + if backend == "serial": + if verbose: + print("Piling up {} dataset(s) serially".format(len(jobs))) + return [_run_one(job, target_partitions, verbose) for job in jobs] + + planned, groups = plan_pileup(len(jobs), _bytes_per_job(jobs)) + if workers is None: + workers = planned + else: + # A caller who names the worker count still gets batches sized + # for it, since the peak has to fit whatever concurrency they + # asked for. + groups = plan_pileup(int(workers), _bytes_per_job(jobs))[1] + workers = max(1, min(int(workers), len(jobs))) + if target_partitions is None: + target_partitions = default_partitions(workers) + # The planner saw the mean, which says nothing about a set holding + # one alignment many times the size of the rest -- and that is the + # one at risk. Each job is raised to what its own bytes ask for, + # rather than every job being sized for the largest: batches cost + # wall clock on small inputs, and the output is byte-identical at + # any count, so there is nothing to lose by letting them differ. + for job in jobs: + job.setdefault("contig_groups", max(groups, _group_floor(_job_bytes(job)))) + + if verbose: + counts = sorted({int(job["contig_groups"]) for job in jobs}) + print( + "Piling up {} dataset(s) across {} {} worker(s), {} " + "partition(s) each, {} contig group(s)".format( + len(jobs), + workers, + backend, + target_partitions, + counts[0] if len(counts) == 1 else "{}-{}".format(counts[0], counts[-1]), + ) + ) + + if backend == "process": + return _run_process(jobs, workers, target_partitions, verbose) + + raise NotImplementedError( + "the 'wool' backend has not been ported to quadrat yet -- see " + "https://github.com/abdenlab/quadrat/issues/1. It dispatches " + "pileups to workers on other machines, and it is the only part " + "of the pileup that needs a dependency outside this package. " + "Use backend='process' to run concurrently on this machine." + ) + + +def _job_bytes(job): + """Alignment bytes one job reads, or None if they cannot be sized. + + The per-job counterpart of :func:`_bytes_per_job`, which answers + for the set. Kept separate rather than factored out of it: that + one divides by the job count and returns None for a set with no + alignments at all, and both edges are pinned by tests. + """ + + total = 0 + for path in job.get("alignments", ()): + try: + total += os.path.getsize(path) + except OSError: + return None + return total or None + + +def _bytes_per_job(jobs): + """Mean alignment bytes a job reads, or None if they cannot be sized. + + The mean rather than the max: workers are long-lived and the sizes in + one set are usually within a factor of two, so sizing every worker to + the largest file would leave most of the machine idle. A set that is + genuinely lopsided is better served by passing ``workers`` outright. + """ + + sizes = [] + for job in jobs: + for path in job.get("alignments", ()): + try: + sizes.append(os.path.getsize(path)) + except OSError: + return None + if not sizes: + return None + return int(sum(sizes) / len(jobs)) + + +def _run_process(jobs, workers, target_partitions, verbose): + """Fan out over a local process pool. + + ``loky`` rather than the default: it starts workers with ``spawn``, + and ``giql_io`` caches a polars-bio FASTA registration in a + process-global that a forked child would inherit as a handle it does + not own. + """ + + from joblib import Parallel, delayed + + return list( + Parallel(n_jobs=workers, backend="loky")( + delayed(_run_one)(job, target_partitions, verbose) for job in jobs + ) + ) diff --git a/src/quadrat/pileup/sql.py b/src/quadrat/pileup/sql.py new file mode 100644 index 0000000..70390d0 --- /dev/null +++ b/src/quadrat/pileup/sql.py @@ -0,0 +1,147 @@ +"""The cut-site aggregate, as one query per contig batch. + +Every mapped record contributes one cut site -- ``start + pos_shift`` +forward, ``end - 1 + neg_shift`` reverse -- and the aggregate counts +them per position. The count is an exact integer scaled once +afterwards, which is what makes two backends byte-comparable rather +than approximately equal. + +The join against contig sizes sits *above* the aggregate, not beside +the reads. Below it, the probe side carries one row per record, and at +291 M records the ``chrom`` array crosses Arrow's 2**31 offset ceiling +and the query dies. Above it, the same filter runs against one row per +distinct position. It is equivalent because ``length`` is a function of +``chrom`` alone and ``chrom`` is a grouping key, so the predicate is +constant across every row of a group: the join can only delete whole +groups, never alter a surviving group's count. + +The sizes table is also named first in ``FROM``, because DataFusion +materialises the left input of a ``CollectLeft`` join whole and the +left input is whichever relation ``FROM`` names first. +""" + +from quadrat._engine import _SIZES_TABLE, _sql_string +from quadrat.alignments import _BAM_START_OFFSET + + +def pileup_sql( + bam_tables, + pos_shift=0, + neg_shift=0, + unstranded=False, + scale_factor=1.0, + sizes_table=_SIZES_TABLE, + contigs=None, +): + """Build the cut-site aggregate over one or more registered BAM tables. + + Mirrors bam2bw: forward reads (``flags & 16 = 0``) cut at ``start + + pos_shift``; reverse reads cut at ``end - 1 + neg_shift``; unmapped records + (``flags & 4``) are skipped; records on contigs absent from the sizes + table are dropped; several files are concatenated before counting. The + one deliberate difference is that cut sites shifted outside ``[0, len)`` + are dropped here, whereas bam2bw hands them to pyBigWig unclipped; no + training window can read those positions, so tensors are unaffected. + + ``contigs`` restricts each branch to the contigs that branch's table + actually has, as ``{table: [chrom, ...]}``. The predicate goes on the + scan rather than on the join because that is what reaches the BAM + index: a contig equality is pushed down to an indexed region query, + so a group costs only the records it selects. A table with nothing + in the group is dropped from the ``UNION ALL`` -- asking its provider + for a region absent from its header raises rather than returning + nothing -- and when no table has anything, the whole query is + ``None``. + + The bound on ``[0, len)`` is applied *after* the aggregate, and the + sizes table is named first in the ``FROM`` clause. Both halves of + that matter. ``length`` is a function of ``chrom`` alone and + ``chrom`` is a grouping key, so the predicate is constant across + every row of a group: the join can only delete whole ``(chrom, + pos)`` groups, never alter a surviving group's count. Joining the + grouped result is therefore the same answer over far fewer rows -- + 16,898,696 groups rather than 291,063,148 reads on the alignment + this was measured against, filtering to the 16,882,300 the pileup + writes either way. Joining the reads used to die outright: + DataFusion plans this as a ``CollectLeft`` hash join and + materialises the left input whole, so one Arrow ``chrom`` array + held every read's contig name and crossed the 32-bit offset + ceiling just past 2^31. Naming the sizes table first keeps the + collected side at one row per contig whatever sits below it. + + The join stays an inner one because it is also the contig filter: + a record on a contig the reference does not name is dropped, and + after the rewrite its whole group is dropped instead. The sizes + table has one row per contig, so it cannot duplicate a grouped row + either. One cost, paid only when ``contigs`` is ``None``: the + aggregate now builds entries for off-reference contigs before the + join deletes them. ``_pileup_group`` always passes a batch and + :func:`_contig_batches` builds its groups from the reference's own + lengths, so nothing off-reference reaches the SQL on that path. + + The ``ORDER BY`` is not cosmetic and is not for the reader, and it + sits on the outermost query, above the join. It puts each strand, + and each contig within a strand, in one contiguous run, which is + what lets :func:`pileup_alignments` and :func:`_write_cut_sites` + take every output file as a zero-copy ``slice`` of the result. The + alternative -- ``filter`` per strand and ``partition_by`` per contig -- + allocates a second and third copy of the whole table, and at ENCODE + scale those copies are the memory bound rather than an overhead. + """ + + strand = ( + "CASE WHEN (CAST(b.flags AS BIGINT) & 16) = 0 THEN '+' ELSE '-' END AS strand" + ) + pos = ( + "CASE WHEN (CAST(b.flags AS BIGINT) & 16) = 0 " + "THEN CAST(b.start AS BIGINT) + {offset} + ({pos_shift}) " + 'ELSE CAST(b."end" AS BIGINT) + {offset} + ({neg_shift}) - 1 END AS pos' + ).format( + offset=_BAM_START_OFFSET, pos_shift=int(pos_shift), neg_shift=int(neg_shift) + ) + + branches = [] + for table in bam_tables: + where = "(CAST(b.flags AS BIGINT) & 4) = 0" + if contigs is not None: + names = list(contigs.get(table, ())) + if not names: + # This table has nothing in this group. Emitting a + # branch anyway would ask its provider for a region it + # has never heard of, which is an error rather than an + # empty result. + continue + where += " AND b.chrom IN ({})".format( + ", ".join(_sql_string(name) for name in names) + ) + branches.append( + "SELECT b.chrom, {pos}, {strand} FROM {table} AS b WHERE {where}".format( + pos=pos, strand=strand, table=table, where=where + ) + ) + + if not branches: + return None + + keys = ["chrom", "pos"] if unstranded else ["chrom", "pos", "strand"] + group = ", ".join("c." + key for key in keys) + select = ", ".join("g." + key for key in keys) + order = ", ".join( + "g." + key for key in (keys if unstranded else ["strand", "chrom", "pos"]) + ) + return ( + "WITH cuts AS ({branches}), " + "counts AS (SELECT {group}, CAST(COUNT(*) AS DOUBLE) * {scale} " + "AS value FROM cuts AS c WHERE c.pos >= 0 GROUP BY {group}) " + "SELECT {select}, g.value " + "FROM {sizes} AS s JOIN counts AS g ON s.chrom = g.chrom " + "WHERE g.pos < s.length " + "ORDER BY {order}" + ).format( + branches=" UNION ALL ".join(branches), + group=group, + select=select, + order=order, + scale=float(scale_factor), + sizes=sizes_table, + ) diff --git a/src/quadrat/reference.py b/src/quadrat/reference.py new file mode 100644 index 0000000..d04d95d --- /dev/null +++ b/src/quadrat/reference.py @@ -0,0 +1,117 @@ +"""Reading a reference: contig lengths and sequence by coordinate. + +Lengths come from the FASTA index when one exists and from a scan when +it does not, because the pileup needs them before it reads a single +alignment -- they are what bounds a cut site to its contig and what a +contig batch is built from. +""" + +import collections + +from quadrat._engine import _cache, _pb, _FASTA_TABLE + + +### +# Sequences +### + + +def _register_fasta(sequences): + """Register ``sequences`` (a FASTA path) once, dropping stale caches.""" + + if not isinstance(sequences, str): + raise NotImplementedError( + "The GIQL engine reads sequences from a " + "FASTA file; in-memory sequence dictionaries are not supported." + ) + + pb = _pb() + if _cache["fasta"] != sequences: + pb.register_fasta(sequences, _FASTA_TABLE) + _cache["fasta"] = sequences + _cache["chrom_lengths"] = None + _cache["sequences"] = {} + return pb + + +def chrom_lengths(sequences): + """Return an ordered ``chrom -> length`` mapping for a FASTA file. + + Read from the faidx index, which stores each contig's length directly, + so no sequence is touched. The polars-bio table scan below computes the + same thing with ``LENGTH(sequence)``, which means materializing the + genome: measured on hg38 that is 4.8 s and a 10.2 GB peak, against + 0.00 s and 0.03 GB from the index, for a byte-identical mapping in the + same order. It dominated the memory profile of an otherwise lazy + pipeline. + + The scan remains the fallback for a FASTA with no ``.fai`` beside it + that cannot be indexed in place. pyfaidx is also the reference + definition here, in the sense that bam2bw and tangermeme take their + lengths the same way. + """ + + if not isinstance(sequences, str): + raise NotImplementedError( + "The GIQL engine reads sequences from a " + "FASTA file; in-memory sequence dictionaries are not supported." + ) + + if _cache.get("chrom_lengths_path") != sequences: + _cache["chrom_lengths"] = None + + if _cache["chrom_lengths"] is None: + lengths = None + try: + import pyfaidx + + fasta = pyfaidx.Fasta(sequences) + try: + lengths = collections.OrderedDict( + (chrom, len(fasta[chrom])) for chrom in fasta.keys() + ) + finally: + fasta.close() + except Exception: + lengths = None + + if lengths is None: + pb = _register_fasta(sequences) + frame = pb.sql( + "SELECT name, LENGTH(sequence) AS length FROM {}".format(_FASTA_TABLE) + ).collect() + lengths = collections.OrderedDict( + zip(frame["name"].to_list(), frame["length"].to_list()) + ) + + _cache["chrom_lengths"] = lengths + _cache["chrom_lengths_path"] = sequences + return _cache["chrom_lengths"] + + +def _prefetch_sequences(sequences, chroms): + """Load every chromosome in ``chroms`` with a single FASTA scan.""" + + pb = _register_fasta(sequences) + missing = [str(c) for c in chroms if str(c) not in _cache["sequences"]] + if not missing: + return + + frame = pb.sql( + "SELECT name, sequence FROM {} WHERE name IN ({})".format( + _FASTA_TABLE, ", ".join("'{}'".format(c) for c in missing) + ) + ).collect() + for name, sequence in zip(frame["name"].to_list(), frame["sequence"].to_list()): + _cache["sequences"][name] = sequence + + +def _chrom_sequence(sequences, chrom): + """Return the residues of one chromosome as a Python string (cached).""" + + chrom = str(chrom) + if chrom not in _cache["sequences"]: + _prefetch_sequences(sequences, [chrom]) + if chrom not in _cache["sequences"]: + raise KeyError(chrom) + return _cache["sequences"][chrom] diff --git a/src/quadrat/tables.py b/src/quadrat/tables.py new file mode 100644 index 0000000..788c554 --- /dev/null +++ b/src/quadrat/tables.py @@ -0,0 +1,555 @@ +"""The cut-site table format, and the atomic writer that produces it. + +A cut-site table is a directory of per-contig Parquet files holding +sorted ``(chrom, pos, value)`` rows, with a completeness manifest +beside it rather than inside it. Beside, because a cut-site directory +must hold Parquet and nothing else: polars refuses to scan a directory +of mixed extensions, and so does anything else pointed at the dataset. + +The format and ``MANIFEST_VERSION`` are deliberately unchanged from +cherimoya's. Tables either package writes are readable by the other, +and the alternative is re-piling every corpus to move between them. +""" + +import json +import os +import shutil +import urllib.parse +import uuid + + +CUT_SITE_SUFFIX = ".cuts.parquet" + + +# Parquet row-group size for the cut-site tables. See `_write_cut_sites` +# for why this number and not a rounder one. +_ROW_GROUP_SIZE = 50_000 + + +# Suffix of the completeness record that sits *beside* a cut-site +# directory, and the schema version it declares. See `_write_cut_sites` +# for what it is for. +# +# Beside, not inside: a cut-site directory must hold Parquet and nothing +# else, because polars refuses to scan a directory of mixed extensions +# and so does anything else pointed at the dataset. That invariant is +# pinned by `test_cut_site_directory_holds_parquet_and_nothing_else`, +# which an earlier memory-mapped read index already broke once. +MANIFEST_SUFFIX = ".manifest.json" + + +MANIFEST_VERSION = 1 + + +# Prefixes for the staging and discard directories the atomic write uses. +# Both are siblings of the final path so the renames stay within one +# filesystem; `_sweep_stale` reaps any left behind by a killed writer. +_STAGING_INFIX = ".staging." + + +_TRASH_INFIX = ".trash." + + +def _chrom_filename(chrom): + """Filesystem-safe filename for one contig. + + ``urllib.parse.quote`` leaves alphanumerics and ``_.-~`` alone, so the + ordinary names stay readable (``chr1.parquet``, + ``chr14_GL000009v2_random.parquet``) while an assembly that ships a + contig with a slash or a space in it still lands on a valid path. + """ + + return urllib.parse.quote(str(chrom), safe="") + ".parquet" + + +def cut_site_chrom_path(source, chrom): + """Path to one chromosome's Parquet file inside a cut-site directory.""" + + return os.path.join(source, _chrom_filename(chrom)) + + +def _sweep_stale(path): + """Remove staging/discard siblings left by an interrupted write. + + A writer killed between ``makedirs`` and the final rename leaves a + ``{path}.staging.{hex}`` directory behind; one killed between the two + renames leaves a ``{path}.trash.{hex}``. Neither is ever read, but + they are the size of a whole channel, so sweeping them at the start of + the next write keeps a crash loop from filling the disk. Failures are + swallowed: a leftover directory someone else is actively writing (two + pileups racing on the same name) is their problem to report, not a + reason to fail this one before it starts. + """ + + parent = os.path.dirname(os.path.abspath(path)) or "." + prefix = os.path.basename(os.path.abspath(path)) + try: + entries = os.listdir(parent) + except OSError: + return + for entry in entries: + if not entry.startswith(prefix): + continue + rest = entry[len(prefix) :] + if not (rest.startswith(_STAGING_INFIX) or rest.startswith(_TRASH_INFIX)): + continue + try: + shutil.rmtree(os.path.join(parent, entry), ignore_errors=True) + except OSError: + pass + + +def manifest_path(source): + """Path to the completeness record that belongs beside ``source``.""" + + return str(source) + MANIFEST_SUFFIX + + +def read_manifest(source): + """Completeness record for a cut-site directory, or ``None``. + + ``None`` means the table predates manifests, is a plain file, or the + record is absent or unreadable -- all of which :func:`require_complete` + treats the same way, because none of them can be distinguished from a + write that did not finish. + """ + + if not isinstance(source, str) or not os.path.isdir(source): + return None + try: + with open(manifest_path(source)) as handle: + manifest = json.load(handle) + except (OSError, ValueError): + return None + if not isinstance(manifest, dict): + return None + return manifest + + +def require_complete(source): + """Raise unless ``source`` is a cut-site table that finished writing. + + The check exists because the reader cannot otherwise tell a truncated + table from a complete one. :func:`_chrom_cut_sites` returns ``None`` + for a chromosome whose file is absent, and that is *correct* for a + contig with no cut sites -- routine for small unplaced ones -- so a + writer killed after chr1-chr8 leaves a directory that reads as valid + and silently trains on a genome missing most of its signal. The + manifest, written last, is the only thing that distinguishes the two. + + There is deliberately no override. A table costs minutes to rebuild + (234 s for twenty BAMs on a 128-core box) and a silently partial one + costs a training run plus however long it takes to doubt the result, + so "read it anyway" is never the right trade. Directories written + before manifests existed fail here and must be rebuilt; they are + genuinely unverifiable, not merely old. + + In-memory frames and single-file tables pass through untouched -- a + frame has no partial state, and a truncated Parquet file fails on its + own footer. + """ + + if not isinstance(source, str) or not os.path.isdir(source): + return source + + manifest = read_manifest(source) + if manifest is None: + raise ValueError( + "{} has no {} beside it and cannot be verified complete. A " + "cut-site directory whose write was interrupted is " + "indistinguishable from one whose contigs are genuinely empty, " + "so it is not safe to train on. Rebuild it by piling up the " + "alignments again.".format(source, os.path.basename(manifest_path(source))) + ) + + version = manifest.get("version") + if version != MANIFEST_VERSION: + raise ValueError( + "{} declares manifest schema version {!r}, but this quadrat " + "writes and reads version {}. Rebuild the table.".format( + source, version, MANIFEST_VERSION + ) + ) + + files = manifest.get("files") or {} + missing = [name for name in files if not os.path.exists(os.path.join(source, name))] + if missing: + raise ValueError( + "{} is missing {} of the {} Parquet files its manifest lists " + "({}). The table has been truncated since it was written; " + "rebuild it.".format( + source, len(missing), len(files), ", ".join(sorted(missing)[:5]) + ) + ) + + # Every file is present, which says nothing about whether the manifest + # describes them correctly. `_CutSiteWriter` increments `rows` and + # records the per-file height from the same frame slice, so the two + # agree by construction and a disagreement means the record did not + # come from one uninterrupted write -- two manifests merged, a hand + # edit, or a writer that is not this one. Cheap to check and the only + # internal consistency the record has. + # + # Guarded on the values being counts because window-cache entries + # share `MANIFEST_VERSION` and list their files with `None`, having no + # row count to record; for those there is nothing to add up. + rows = manifest.get("rows") + counts = list(files.values()) + if isinstance(rows, int) and all(isinstance(n, int) for n in counts): + total = sum(counts) + if total != rows: + raise ValueError( + "{} has a manifest that does not add up: its {} files " + "declare {} rows between them but the manifest records " + "{} in total. The record does not describe a single " + "finished write; rebuild the table.".format( + source, len(files), total, rows + ) + ) + + return source + + +def _runs(frame, column): + """Contiguous ``(value, offset, length)`` runs of one column. + + A frame grouped by that column -- which is what the pileup's + ``ORDER BY`` delivers -- has exactly one run per distinct value, and a + run is exactly the rows one output file needs. Taking it with + ``slice`` is a view over the same Arrow buffers; ``filter`` and + ``partition_by`` both allocate a second copy of everything they are + handed, which is the difference between holding the result once and + holding it three times. + """ + + runs = [] + offset = 0 + for entry in frame.get_column(column).rle(): + length = int(entry["len"]) + runs.append((entry["value"], offset, length)) + offset += length + return runs + + +class _CutSiteWriter(object): + """One cut-site table, assembled from one or more frames. + + The pileup runs the genome in contig groups so that it holds only + part of the aggregate at a time, and so hands a table over in + several disjoint pieces rather than one. The staging directory, the + file list and the commit belong to a *writer*, not to a path: two + separate writers on the same path still replace one another + wholesale, which is what lets :func:`_write_cut_sites` keep meaning + exactly what it meant before groups existed. + + No frame is retained. Every part written is a zero-copy ``slice`` of + the caller's frame, so holding one would pin the whole group and + give back the memory the grouping exists to save; only a filename + and a row count are kept. + + Use it as a context manager. A writer abandoned without one leaks + its staging directory until the next `_sweep_stale`, which is the + same exposure a killed process has always had. + """ + + def __init__(self, path, parameters=None): + # Sweep before the staging directory exists, and exactly once: + # `_sweep_stale` reaps every `{path}.staging.*` sibling, which + # would include ours if it ran afterwards. + _sweep_stale(path) + self.path = path + self.rows = 0 + self.parameters = dict(parameters or {}) + self._marker = manifest_path(path) + self._files = {} + self._staging = "{}{}{}".format(path, _STAGING_INFIX, uuid.uuid4().hex) + os.makedirs(self._staging) + + def __enter__(self): + return self + + def __exit__(self, kind, value, trace): + if self._staging is None: + return False + if kind is None: + self.commit() + else: + self.abort() + return False + + def write(self, frame): + """Stage one frame's contigs. + + The frame must cover contigs no earlier frame covered. That is + checked rather than assumed, because writing a contig twice + fails silently: the second file replaces the first, ``rows`` + counts both, and the table still verifies, so training would + read a contig that is missing half its cut sites and nothing + would say so. + """ + + if self._staging is None: + raise RuntimeError("{} is already closed".format(self.path)) + + try: + runs = _runs(frame, "chrom") + if len({chrom for chrom, _, _ in runs}) != len(runs): + # A contig appears in more than one run, so the slices + # below would write the same filename twice. The pileup + # never lands here -- its ORDER BY guarantees one run + # per contig -- but the eager helpers and the tests + # build frames in whatever order suits them, and pay + # one sort for it. It sorts a group, not the genome. + frame = frame.sort("chrom", "pos") + runs = _runs(frame, "chrom") + + for chrom, offset, length in runs: + name = _chrom_filename(chrom) + if name in self._files: + raise ValueError( + "{} was already written to {}; the frames given " + "to one cut-site writer must cover disjoint " + "contigs".format(chrom, self.path) + ) + part = frame.slice(offset, length) + if not part.get_column("pos").is_sorted(): + part = part.sort("pos") + part.write_parquet( + os.path.join(self._staging, name), + row_group_size=_ROW_GROUP_SIZE, + statistics=True, + ) + self._files[name] = part.height + self.rows += part.height + except BaseException: + self.abort() + raise + + def commit(self): + """Swap the staged directory in and mark it complete.""" + + if self._staging is None: + raise RuntimeError("{} is already closed".format(self.path)) + staging, self._staging = self._staging, None + + # Invalidate the old table before touching it, so a crash + # anywhere below leaves something that refuses to be read + # rather than a new directory wearing a previous write's + # manifest. + try: + os.remove(self._marker) + except FileNotFoundError: + pass + + trash = None + if os.path.isdir(self.path): + trash = "{}{}{}".format(self.path, _TRASH_INFIX, uuid.uuid4().hex) + os.replace(self.path, trash) + elif os.path.exists(self.path): + os.remove(self.path) + + try: + os.replace(staging, self.path) + except BaseException: + # Put the previous table back; a failed rebuild should not + # also destroy what was already there. It stays + # unverifiable, because its manifest is already gone and we + # cannot reconstruct one we did not write. + if trash is not None and not os.path.exists(self.path): + os.replace(trash, self.path) + trash = None + shutil.rmtree(staging, ignore_errors=True) + raise + + manifest = { + "version": MANIFEST_VERSION, + "rows": int(self.rows), + "files": self._files, + "parameters": self.parameters, + } + # The manifest is the completeness marker, so it must land + # whole: a reader must never be able to parse a half-flushed + # JSON object. + with open(self._marker + ".tmp", "w") as handle: + json.dump(manifest, handle, indent=1, sort_keys=True) + os.replace(self._marker + ".tmp", self._marker) + + if trash is not None: + shutil.rmtree(trash, ignore_errors=True) + + def abort(self): + """Discard whatever was staged. A no-op once closed.""" + + staging, self._staging = self._staging, None + if staging is not None: + shutil.rmtree(staging, ignore_errors=True) + + +def _write_cut_sites(path, frame, parameters=None): + """Write one channel as a directory of per-chromosome Parquet files. + + ``path`` keeps its ``.cuts.parquet`` name but is a *directory*, so every + caller that builds these names from `CUT_SITE_SUFFIX` -- + `_cut_site_paths` and anything downstream that reads the emitted + manifest -- is unaffected. + + Sorted per chromosome with 50,000-row groups, which is what lets the + whole table be scanned and grouped into a + :class:`WindowSignalCache` in well under a second. Both choices were + measured on ENCSR483RKN (26.2M cut sites): against the previous single + file with 1,000,000-row groups, a windowed read went from 6.7 ms to + 0.78 ms, and smaller groups are not better -- 10,000 regresses to + 2.2 ms as per-group metadata outweighs what it prunes. + + Training no longer reads a window out of here directly, so that figure + now bounds the one-off grouping pass rather than every sample. It still + matters for the eager extractor and the outlier aggregate, which do + scan these files. + + The dtypes are deliberately left as Int64/Float64. Narrowing ``pos`` to + Int32 and ``value`` to UInt16 *doubles* the file on disk, because + sorted Int64 positions delta-encode far better than Int32 ones; the + cache narrows them in memory instead, where it is free. + + Each contig is taken as a ``slice`` of ``frame`` rather than a + ``partition_by`` entry. ``partition_by(as_dict=True)`` builds every + contig at once while the parent is still alive, so it doubles the + footprint of a table that is already the largest thing in the + process; a slice is a view over the same buffers and costs nothing. + This requires the frame to be grouped by contig, which the pileup's + ``ORDER BY`` guarantees and which is checked rather than assumed -- + an ungrouped frame is sorted once and then sliced the same way. + + The ``chrom`` column is kept inside each file even though the filename + already implies it. It costs nothing once dictionary-encoded and it keeps + the eager `extract_signal` path, which filters on ``chrom``, working + against a globbed scan of the directory. + + The directory is assembled under a ``.staging.{hex}`` sibling and moved + into place with ``os.replace``, which is atomic within a filesystem -- + the staging sibling guarantees that by construction, and it is also + what keeps the scheme sound on NFS, where directory rename is atomic + in practice but not by contract. + + The manifest is written *after* that swap, and the stale one is + removed *before* it, so the commit order is: table unverifiable, + table replaced, table verifiable. Every crash point therefore leaves + the table failing :func:`require_complete` rather than silently + readable, which is the direction this is allowed to fail in. The cost + is that a successful write is briefly complete-but-unverifiable; the + manifest is a few hundred bytes, so that window is a single small + write long. + + ``parameters`` is recorded in the manifest so a table carries the + pileup arguments that produced it; see :func:`require_complete` for + what the manifest is for. + + This is the whole-table form. The pileup runs the genome in contig + groups and so drives :class:`_CutSiteWriter` directly, giving it one + frame per group and committing once at the end; the two produce + byte-identical tables. + """ + + with _CutSiteWriter(path, parameters=parameters) as writer: + writer.write(frame) + + +def _strand_slices(frame, unstranded): + """The rows of each output channel, as views over ``frame``. + + Stranded output used to come from two ``filter`` calls, each + allocating half the table, and then a sort allocating half again -- + all while the parent frame was still referenced. Since the SQL orders + by strand first, each channel is one contiguous run, and ``slice`` + returns it without copying. A strand with no reads yields an empty + frame, as the filter did. + """ + + columns = ["chrom", "pos", "value"] + if unstranded: + return [frame.select(columns)] + + spans = { + strand: (offset, length) for strand, offset, length in _runs(frame, "strand") + } + return [ + frame.slice(*spans.get(strand, (0, 0))).select(columns) for strand in ("+", "-") + ] + + +def _cut_site_paths(name, unstranded): + if unstranded: + return [name + CUT_SITE_SUFFIX] + return [name + ".+" + CUT_SITE_SUFFIX, name + ".-" + CUT_SITE_SUFFIX] + + +### +# Loci +### + + +def _cut_site_frame(source): + """Normalize one cut-site source to a polars LazyFrame. + + A source is either a path to a ``.cuts.parquet`` table written by + :func:`pileup_alignments`, or an in-memory polars ``DataFrame`` / + ``LazyFrame`` with the same ``chrom, pos, value`` columns. The in-memory + form is what lets a caller run BAM to tensors without touching disk. + + ``.cuts.parquet`` is a directory of per-chromosome files (see + :func:`_write_cut_sites`); it is globbed back into one frame here because + this eager path filters on ``chrom`` and wants every contig visible at + once. A plain file is still accepted so tables written before the layout + change keep loading. + """ + + import polars + + if isinstance(source, str): + if os.path.isdir(source): + require_complete(source) + return polars.scan_parquet(os.path.join(source, "*.parquet")) + return polars.scan_parquet(source) + if isinstance(source, polars.LazyFrame): + return source + if isinstance(source, polars.DataFrame): + return source.lazy() + + raise NotImplementedError( + "The GIQL engine reads signals from {} tables " + "or in-memory polars frames; got {!r}".format( + CUT_SITE_SUFFIX, type(source).__name__ + ) + ) + + +def cut_site_contigs(source): + """Every contig a cut-site source holds at least one row for. + + The directory layout answers from its filenames: `_write_cut_sites` + writes one file per contig run and none at all for a contig with no + rows, so for the tables training reads this costs a listing and no + bytes. The manifest is preferred over the listing when there is + one, because :func:`require_complete` has already checked those + names against the disk. A single-file table or an in-memory frame + has to be asked, which reads the ``chrom`` column and nothing else. + + The counterpart of :func:`bam_contigs` on the other side of the + pileup, and what :func:`_require_signal_contigs` compares against. + """ + + if isinstance(source, str) and os.path.isdir(source): + manifest = read_manifest(source) + names = list((manifest.get("files") or {}) if manifest else []) + if not names: + names = [name for name in os.listdir(source) if name.endswith(".parquet")] + return {urllib.parse.unquote(name[: -len(".parquet")]) for name in names} + + frame = _cut_site_frame(source) + return set(frame.select("chrom").unique().collect()["chrom"].to_list()) + + +def _source_name(source): + """How to name a cut-site source in a message.""" + + return source if isinstance(source, str) else "an in-memory frame" diff --git a/tests/_builders.py b/tests/_builders.py index 88eb28a..ea26433 100644 --- a/tests/_builders.py +++ b/tests/_builders.py @@ -130,9 +130,14 @@ def write_random_bam(path, header, chrom_sizes, *, n_reads=40, seed=0, read_leng rng = random.Random(seed) chroms = list(chrom_sizes) + # The first contig twice as often as the others, so a contig batch + # split is not uniform and a per-contig count is not the same number + # everywhere. Cycled rather than drawn, so the spread does not + # depend on how many reads were asked for. + pool = [chroms[0]] * 2 + chroms reads = [] for index in range(n_reads): - chrom = chroms[0] if index % 3 else chroms[index % len(chroms)] + chrom = pool[index % len(pool)] span = chrom_sizes[chrom] - read_length * 2 reads.append( aligned_read( diff --git a/tests/test_builders.py b/tests/test_builders.py index 4fa503a..8840ebe 100644 --- a/tests/test_builders.py +++ b/tests/test_builders.py @@ -12,6 +12,7 @@ with nothing else. """ +import collections import gzip import os @@ -355,3 +356,33 @@ def test_conftest_should_point_the_cache_at_a_temporary_directory(): assert os.path.isdir(cache_dir) assert "quadrat-test-cache-" in cache_dir assert not cache_dir.startswith(os.path.expanduser("~/.cache")) + + +def test_write_random_bam_should_spread_reads_over_every_contig(tmp_path): + """Test that a random BAM reaches every contig, unevenly. + + Given: + A header over three contigs and enough reads to cover them. + When: + write_random_bam places them. + Then: + It should put reads on all three, and more on the first than on + either of the others -- a corpus confined to one contig cannot + exercise contig batching at all, which is the whole reason the + pileup splits the genome. + """ + + # Arrange + sizes = {"chr1": 2000, "chr2": 1500, "chr3": 1000} + header = _builders.alignment_header(sizes) + path = str(tmp_path / "spread.bam") + + # Act + _builders.write_random_bam(path, header, sizes, n_reads=60) + + # Assert + with pysam.AlignmentFile(path, "rb") as bam: + counts = collections.Counter(read.reference_name for read in bam.fetch()) + assert set(counts) == set(sizes) + assert counts["chr1"] > counts["chr2"] + assert counts["chr1"] > counts["chr3"] diff --git a/tests/test_pileup.py b/tests/test_pileup.py new file mode 100644 index 0000000..bf2f794 --- /dev/null +++ b/tests/test_pileup.py @@ -0,0 +1,972 @@ +"""Tests for running many cut-site pileups at once. + +Ported from cherimoya's ``tests/test_pileup.py``, which held the whole data path in +one module. The names it reached for as ``giql_io.x`` and +``pileup.x`` are spread over several modules here, so the references +are rewritten and nothing else is: the assertions are the evidence +that the split preserved behaviour, and rewriting them in the same +change that moves them would destroy that evidence. + +Style follows cherimoya rather than this project's test conventions -- +natural-language names, no Arrange-Act-Assert phases. Converting them +is a separate change, tracked on the epic. +""" + +import hashlib +import os +import random +import shutil +import warnings + +import pytest + +pytest.importorskip("polars_bio") +pysam = pytest.importorskip("pysam") +polars = pytest.importorskip("polars") + + +from quadrat import alignments, tables +from quadrat import pileup as pileup_pkg +from quadrat.pileup import plan, run + +os.environ.setdefault("TQDM_DISABLE", "1") + +CHROM_SIZES = {"chr1": 1000, "chr2": 500} + + +@pytest.fixture(scope="module") +def data_dir(tmp_path_factory): + return tmp_path_factory.mktemp("pileup") + + +@pytest.fixture(scope="module") +def fasta(data_dir): + rng = random.Random(0) + path = str(data_dir / "genome.fa") + with open(path, "w") as f: + for chrom, size in CHROM_SIZES.items(): + seq = "".join(rng.choice("ACGT") for _ in range(size)) + f.write(">{}\n".format(chrom)) + for i in range(0, size, 60): + f.write(seq[i : i + 60] + "\n") + pysam.faidx(path) + return path + + +@pytest.fixture(scope="module") +def bams(data_dir): + """Four small BAMs, each with a different read layout.""" + + header = pysam.AlignmentHeader.from_dict( + { + "HD": {"VN": "1.6", "SO": "coordinate"}, + "SQ": [{"SN": "chr1", "LN": 1000}, {"SN": "chr2", "LN": 500}], + } + ) + + paths = [] + for index in range(4): + rng = random.Random(index) + reads = [] + for i in range(40): + chrom = "chr1" if i % 3 else "chr2" + start = rng.randrange(0, CHROM_SIZES[chrom] - 40) + read = pysam.AlignedSegment(header) + read.query_name = "r{}_{}".format(index, i) + read.flag = 16 if i % 2 else 0 + read.reference_id = header.get_tid(chrom) + read.reference_start = start + read.cigarstring = "20M" + read.query_sequence = "A" * 20 + read.query_qualities = pysam.qualitystring_to_array("I" * 20) + read.mapping_quality = 30 + reads.append(read) + + path = str(data_dir / "s{}.bam".format(index)) + unsorted = path + ".unsorted.bam" + with pysam.AlignmentFile(unsorted, "wb", header=header) as out: + for read in sorted(reads, key=lambda r: (r.reference_id, r.reference_start)): + out.write(read) + pysam.sort("-o", path, unsorted) + pysam.index(path) + os.remove(unsorted) + paths.append(path) + return paths + + +def _jobs(bams, fasta, out, prefix, unstranded=True): + return [ + { + "alignments": [bam], + "sequences": fasta, + "name": os.path.join(str(out), "{}{}".format(prefix, i)), + "unstranded": unstranded, + "pos_shift": 4, + "neg_shift": -4, + } + for i, bam in enumerate(bams) + ] + + +def _digest(table): + """sha256 of every Parquet file in a cut-site table, by name. + + The manifest is excluded: it records absolute input paths, which + differ between runs into different directories, and it is not what + the model reads.""" + + out = {} + for name in sorted(os.listdir(table)): + with open(os.path.join(table, name), "rb") as handle: + out[name] = hashlib.sha256(handle.read()).hexdigest() + return out + + +def test_backends_should_write_byte_identical_tables(bams, fasta, tmp_path): + """GIVEN the same jobs run serially and across a process pool + WHEN the written tables are hashed + THEN every Parquet file is byte-for-byte the same. + + This is the whole contract: a backend is a scheduling choice, not a + numerical one. It holds exactly because the aggregate is an integer + COUNT(*) scaled once after grouping, so no partition order can + accumulate floats differently.""" + + a, b = tmp_path / "serial", tmp_path / "process" + a.mkdir() + b.mkdir() + + serial = run.pileup_many(_jobs(bams, fasta, a, "x"), backend="serial") + parallel = run.pileup_many(_jobs(bams, fasta, b, "x"), backend="process", workers=2) + + assert [os.path.basename(p) for group in serial for p in group] == [ + os.path.basename(p) for group in parallel for p in group + ] + + for lhs, rhs in zip(serial, parallel): + for left, right in zip(lhs, rhs): + assert _digest(left) == _digest(right) + assert _digest(left), "table wrote no Parquet files" + + +def test_every_table_is_verifiable_after_a_parallel_run(bams, fasta, tmp_path): + """GIVEN jobs run across a process pool + WHEN each written table is checked for completeness + THEN all of them pass. + + Each pileup commits its own table atomically, so concurrency must not + leave any of them unverifiable.""" + + jobs = _jobs(bams, fasta, tmp_path, "x") + for group in run.pileup_many(jobs, backend="process", workers=2): + for table in group: + assert tables.require_complete(table) == table + assert tables.read_manifest(table)["rows"] > 0 + + +def test_stranded_jobs_keep_channel_order(bams, fasta, tmp_path): + """GIVEN stranded jobs run across a process pool + WHEN the returned paths are inspected + THEN each job yields its plus table before its minus table.""" + + jobs = _jobs(bams, fasta, tmp_path, "s", unstranded=False) + groups = run.pileup_many(jobs, backend="process", workers=2) + + for group in groups: + assert len(group) == 2 + assert group[0].endswith(".+" + tables.CUT_SITE_SUFFIX) + assert group[1].endswith(".-" + tables.CUT_SITE_SUFFIX) + + +def test_results_come_back_in_job_order(bams, fasta, tmp_path): + """GIVEN jobs whose names make their order recoverable + WHEN they are run concurrently + THEN the results are in submission order, not completion order.""" + + jobs = _jobs(bams, fasta, tmp_path, "ordered") + groups = run.pileup_many(jobs, backend="process", workers=3) + + assert [os.path.basename(group[0]) for group in groups] == [ + "ordered{}{}".format(i, tables.CUT_SITE_SUFFIX) for i in range(len(jobs)) + ] + + +def test_target_partitions_is_divided_among_workers(): + """GIVEN a worker count + WHEN the default partition count is computed + THEN the machine is divided rather than claimed by each worker. + + The setting is process-global in DataFusion, so eight pileups each + asking for every core would oversubscribe the thread pool eightfold.""" + + cpus = plan._n_cpus() + assert plan.default_partitions(1) == cpus + assert plan.default_partitions(cpus) == 1 + assert plan.default_partitions(2) == max(1, cpus // 2) + # Never zero, however many workers are asked for. + assert plan.default_partitions(cpus * 100) == 1 + + +def test_the_memory_bound_scales_with_the_input(monkeypatch): + """GIVEN jobs whose alignments differ in size + WHEN the default worker count is computed + THEN the budget tracks the input rather than a fixed guess. + + A pileup peaks at roughly three times the bytes it reads, so what is + safe for a 300 MB alignment is fatal for a 4 GB one. The constant + this replaced said 2 GB regardless, which on a 64 GB machine admitted + 32 workers against a real need of about 380 GB. + + The bound is now something to spend rather than only to obey: a + large input is split into contig batches until it fits, instead of + the machine simply running fewer pileups.""" + + # Pin the machine so the test does not depend on the host. + monkeypatch.setattr(plan, "_n_cpus", lambda: 64) + monkeypatch.setattr( + plan.os, + "sysconf", + lambda name: {"SC_PAGE_SIZE": 4096, "SC_PHYS_PAGES": (64 * 1024**3) // 4096}[ + name + ], + ) + + big, big_groups = plan.plan_pileup(32, 4 * 1024**3) + small, small_groups = plan.plan_pileup(32, 256 * 1024**2) + + assert big < small, "a larger input must not permit more workers" + # A 4 GB input needs 8 GB in one batch, so the budget admits four + # pileups at once -- which is what this did before contig batches + # existed. Splitting it five ways brings the peak to 3.2 GB and so + # buys back most of the machine. + assert big > 4 + assert big_groups > 1 + + # A small input is not split, because what the batches divide is + # only the part of the peak that follows the input, and on a + # 256 MB alignment that part is already small beside the fixed + # cost of running a worker at all. Splitting anyway would buy a + # few percent more concurrency for a quarter more wall clock. + assert small_groups == 1 + + # Nor does it reach the job count: thirty-two workers would cost + # 64 GB in fixed per-worker memory alone, which is the whole + # machine. The bound that binds here is the one the single-multiple + # model had no way to express. + assert small < 32 + assert small * plan.PEAK_BYTES_PER_WORKER <= plan._memory_budget() + + +def test_the_memory_bound_is_conservative_without_sizes(monkeypatch): + """GIVEN jobs whose alignments cannot be sized + WHEN the default worker count is computed + THEN it falls back to the measured per-worker figure. + + Better to under-subscribe a machine than to guess low and have the + run die partway.""" + + monkeypatch.setattr(plan, "_n_cpus", lambda: 64) + monkeypatch.setattr( + plan.os, + "sysconf", + lambda name: {"SC_PAGE_SIZE": 4096, "SC_PHYS_PAGES": (64 * 1024**3) // 4096}[ + name + ], + ) + + workers, groups = plan.plan_pileup(32) + # Twelve GB per worker ungrouped, so four at once on a 64 GB + # machine; batches bring that down without ever guessing the peak + # is smaller than it is. + assert plan.projected_peak(None) == plan.UNKNOWN_INPUT_PEAK_BYTES + assert 4 <= workers < 32 + assert groups > 1 + + +def test_the_core_count_is_the_allocation_not_the_machine(monkeypatch): + """GIVEN a process restricted to part of the machine + WHEN the usable core count is read + THEN it is the restriction, not what the machine has. + + A pileup is usually launched under something that confines it -- + SLURM, a cgroup, a container quota, `taskset` -- and `cpu_count` + reports the whole node whatever the allocation. Believing it sets + `target_partitions` to a parallelism the job cannot have and lets + the worker cap oversubscribe by the restriction's factor. Measured + on js031 under `taskset`, the harness went on recording 256 cores + while confined to 32.""" + + monkeypatch.setattr( + plan.os, "sched_getaffinity", lambda pid: set(range(8)), raising=False + ) + monkeypatch.setattr(plan.os, "cpu_count", lambda: 256) + assert plan._n_cpus() == 8 + + # Where the platform has no affinity call, the machine is the only + # answer there is. + monkeypatch.delattr(plan.os, "sched_getaffinity", raising=False) + assert plan._n_cpus() == 256 + + +def _machine(monkeypatch, cores, ram_gb): + monkeypatch.setattr(plan, "_n_cpus", lambda: cores) + monkeypatch.setattr( + plan.os, + "sysconf", + lambda name: {"SC_PAGE_SIZE": 4096, "SC_PHYS_PAGES": (ram_gb * 1024**3) // 4096}[ + name + ], + ) + + +def test_the_peak_keeps_a_part_the_batches_cannot_divide(): + """GIVEN a projected peak at several batch counts + WHEN the batch count rises + THEN only the part that follows the input falls, and it falls in + proportion rather than as a square root. + + The single multiple this replaced had nowhere to put the engine, + the interpreter and the buffers a worker holds whatever it reads, + so it believed eight batches made all of it nearly three times + smaller. Measured across the twelve arms in + `scripts/results/ladder-after-fix/`, that part does not move.""" + + fixed = plan.PEAK_BYTES_PER_WORKER + ratio = plan.PEAK_BYTES_PER_INPUT_BYTE + job = 8 * 1024**3 + + assert plan.projected_peak(job, 1) == fixed + int(job * ratio) + + # In proportion: four batches scan a quarter of the bytes and hold + # a quarter of the distinct positions. + quarter = plan.projected_peak(job, 4) - fixed + assert quarter == pytest.approx(int(job * ratio) // 4, rel=1e-6) + + # And the floor is the fixed part, however far it is split. + assert plan.projected_peak(job, 1024) > fixed + assert plan.projected_peak(job, 1024) < fixed * 1.01 + + +def test_the_machine_cost_comes_off_the_budget_not_each_worker(monkeypatch): + """GIVEN two machines with the same memory and different core counts + WHEN the budget the workers share is computed + THEN the larger one reserves more, because what the engine holds + per core is spent once rather than once per worker. + + Measured by confining the process tree with `taskset` and changing + nothing else: at twelve workers and eight partitions the peak goes + 50.2, 62.4, 70.0 and 73.8 GB at 32, 64, 128 and 256 cores. Holding + the cores and sweeping `target_partitions` 4 to 32 instead moves it + 72.0 to 76.8 GB, inside the replicate spread -- so the cost follows + the cores and not the partitions, and not the fan-out either.""" + + _machine(monkeypatch, 16, 256) + small = plan._memory_budget() + _machine(monkeypatch, 256, 256) + large = plan._memory_budget() + + assert large < small + assert small - large == 240 * plan.PEAK_BYTES_PER_CORE + + # Never negative, however many cores sit on a small machine. + _machine(monkeypatch, 4096, 8) + assert plan._memory_budget() >= 1 + + +def test_batches_are_not_bought_for_a_marginal_gain(monkeypatch): + """GIVEN an input small enough that the fixed cost dominates + WHEN the batch count is planned + THEN it stays at one, because splitting buys a few percent of + concurrency for a quarter more wall clock. + + The part of the peak the batches divide can always be driven to + nearly nothing, so without this the planner takes every batch it + is allowed on inputs where none of them help.""" + + _machine(monkeypatch, 64, 64) + + workers, groups = plan.plan_pileup(32, 256 * 1024**2) + assert groups == 1 + + # Not because splitting was unavailable -- it would have admitted + # more workers, just not enough more to be worth the wall clock. + assert plan.plan_pileup(32, 256 * 1024**2) == (workers, 1) + more = 0 + for g in range(2, plan.MAX_CONTIG_GROUPS + 1): + fits = plan._memory_budget() // plan.projected_peak(256 * 1024**2, g) + more = max(more, min(32, fits)) + assert workers < more < workers * plan.CONTIG_GROUP_GAIN + + # Where the gain is real it is still taken: a 4 GB input is split, + # because one batch of it admits far fewer workers than several. + big, big_groups = plan.plan_pileup(32, 4 * 1024**3) + whole = plan._memory_budget() // plan.projected_peak(4 * 1024**3, 1) + assert big_groups > 1 + assert big >= whole * plan.CONTIG_GROUP_GAIN + + +def _roomy(monkeypatch): + # js031, where the overflow was found: 256 cores and 1007 GB, which + # is enough memory that the planner never had to split anything. + monkeypatch.setattr(plan, "_n_cpus", lambda: 256) + monkeypatch.setattr( + plan.os, + "sysconf", + lambda name: {"SC_PAGE_SIZE": 4096, "SC_PHYS_PAGES": (1007 * 1024**3) // 4096}[ + name + ], + ) + + +def test_the_scan_cap_counts_batches_from_the_bytes(monkeypatch): + """GIVEN an input size + WHEN the batch floor is computed + THEN it is the fewest batches keeping one scan under the cap.""" + + cap = plan.MAX_GROUP_INPUT_BYTES + assert plan._group_floor(None) == 1 + assert plan._group_floor(0) == 1 + assert plan._group_floor(cap) == 1 + assert plan._group_floor(cap + 1) == 2 + + # The ceiling is real and the floor does not pretend otherwise: past + # `MAX_CONTIG_GROUPS` batches it asks for no more than it can get. + assert plan._group_floor(1024**4) == plan.MAX_CONTIG_GROUPS + + +def test_a_large_job_is_split_however_large_the_machine_is(monkeypatch): + """GIVEN a machine with memory to spare and one very large input + WHEN the pileup is planned + THEN the genome is split anyway, because the bound that matters is + how much one query scans rather than how much memory is free. + + Solving from headroom alone answers one batch here, which is how a + 21.2 GB alignment came to be read as a single aggregate over + 291,063,148 records.""" + + _roomy(monkeypatch) + + assert plan.plan_pileup(1, int(21.2 * 1024**3)) == (1, 3) + + # And not otherwise: batches cost 25% of the pileup wall clock at + # the sizes the ladder measured, so the cap must stay clear of them. + assert plan.plan_pileup(1, 2 * 1024**3)[1] == 1 + + +def test_a_lopsided_job_set_splits_only_the_large_jobs( + bams, fasta, tmp_path, monkeypatch +): + """GIVEN a job set whose mean size is small and one job enormous + WHEN the fan-out is planned + THEN the large job is split and the small ones are left whole. + + The planner is handed the mean, which on a set like this is small: + the rung-3 benchmark set averaged 3.28 GB across 68 alignments and + held one of 21.2 GB, and it was that one that died. A cap read + from the mean alone would have missed it. A job whose caller + pinned a count keeps it.""" + + _roomy(monkeypatch) + + # Five small jobs against two of 24 GB keeps the mean under the cap, + # so nothing but the large jobs own bytes can be what splits them. + small = [] + for i in range(5): + path = str(tmp_path / "small{}.bam".format(i)) + shutil.copy(bams[i % len(bams)], path) + small.append(path) + huge = str(tmp_path / "huge.bam") + shutil.copy(bams[0], huge) + pinned = str(tmp_path / "pinned.bam") + shutil.copy(bams[0], pinned) + + real = run.os.path.getsize + monkeypatch.setattr( + run.os.path, + "getsize", + lambda path: 24 * 1024**3 if path in (huge, pinned) else real(path), + ) + + seen = [] + # `_run_process` rather than `_run_one`: the real one dispatches + # through loky, so a patched callable never reaches the children. + monkeypatch.setattr( + run, "_run_process", lambda jobs, *a, **k: seen.extend(jobs) or [] + ) + + jobs = [ + { + "name": str(tmp_path / "s{}".format(i)), + "alignments": [path], + "sequences": fasta, + } + for i, path in enumerate(small) + ] + jobs.append( + {"name": str(tmp_path / "huge"), "alignments": [huge], "sequences": fasta} + ) + jobs.append( + { + "name": str(tmp_path / "pinned"), + "alignments": [pinned], + "sequences": fasta, + "contig_groups": 1, + } + ) + run.pileup_many(jobs, backend="process") + + groups = {os.path.basename(job["name"]): job["contig_groups"] for job in seen} + assert groups["huge"] == 3, "the 24 GB job must be split" + assert all(groups["s{}".format(i)] == 1 for i in range(5)), ( + "a small job must not be split for its neighbour's sake" + ) + assert groups["pinned"] == 1, "an explicit count must survive the cap" + + +def test_job_sizes_reach_the_worker_count(bams, fasta, tmp_path, monkeypatch): + """GIVEN a job list whose alignments are on disk + WHEN pileup_many plans the fan-out + THEN it sizes the budget from those files. + + The sizes are available at the call site, so a caller who does not + name a worker count should still get a bound fitted to their data.""" + + seen = {} + real = plan.plan_pileup + + def spy(n_jobs, bytes_per_job=None): + seen["bytes_per_job"] = bytes_per_job + return real(n_jobs, bytes_per_job) + + monkeypatch.setattr(run, "plan_pileup", spy) + jobs = _jobs(bams, fasta, tmp_path, "sized") + run.pileup_many(jobs, backend="process") + + assert seen["bytes_per_job"] is not None and seen["bytes_per_job"] > 0 + + +def test_unsizable_alignments_fall_back(tmp_path): + """GIVEN a job naming an alignment that is not on disk + WHEN the per-job size is taken + THEN it is None rather than an error or a wrong number.""" + + assert run._bytes_per_job([{"alignments": [str(tmp_path / "absent.bam")]}]) is None + assert run._bytes_per_job([{"alignments": []}]) is None + + +def test_default_workers_never_exceeds_the_job_count(): + """GIVEN fewer jobs than cores + WHEN the default worker count is computed + THEN it is capped at the number of jobs.""" + + assert plan.default_workers(0) == 0 + assert plan.default_workers(1) == 1 + assert plan.default_workers(3) <= 3 + + +def test_unknown_backend_is_rejected_by_name(): + """GIVEN an unrecognized backend + WHEN pileup_many is called + THEN it names the backends that do exist.""" + + with pytest.raises(ValueError, match="serial, process"): + run.pileup_many([], backend="dask") + + +def test_malformed_jobs_are_rejected_before_any_work(bams, fasta, tmp_path): + """GIVEN a job missing a required argument + WHEN pileup_many is called + THEN it fails naming the job and the argument, before dispatching. + + Validating up front matters more for the concurrent backends: a + KeyError raised inside a worker after fifteen minutes of other jobs + is a far worse way to learn the job list was wrong.""" + + jobs = _jobs(bams, fasta, tmp_path, "x") + del jobs[2]["sequences"] + with pytest.raises(KeyError, match="job 2"): + run.pileup_many(jobs, backend="process", workers=2) + + with pytest.raises(TypeError, match="job 0"): + run.pileup_many(["not-a-dict"], backend="serial") + + assert not os.listdir(tmp_path) + + +def test_empty_job_list_is_a_no_op(): + """GIVEN no jobs + WHEN pileup_many is called + THEN it returns nothing without starting a pool.""" + + for backend in run.BACKENDS: + assert run.pileup_many([], backend=backend) == [] + + +### +# Contig grouping +# +# Splitting the genome into batches is a memory optimisation and must be +# nothing else, so the tests here are about equality with the ungrouped +# form rather than about the peak -- a byte comparison is checkable in +# CI, where a memory figure is not. +### + + +def _one_contig_bam(path, chrom="chr1", size=1000, reads=20): + header = pysam.AlignmentHeader.from_dict( + { + "HD": {"VN": "1.6", "SO": "coordinate"}, + "SQ": [{"SN": chrom, "LN": size}], + } + ) + rng = random.Random(99) + out = [] + for i in range(reads): + read = pysam.AlignedSegment(header) + read.query_name = "solo{}".format(i) + read.flag = 16 if i % 2 else 0 + read.reference_id = 0 + read.reference_start = rng.randrange(0, size - 40) + read.cigarstring = "20M" + read.query_sequence = "A" * 20 + read.query_qualities = pysam.qualitystring_to_array("I" * 20) + read.mapping_quality = 30 + out.append(read) + + unsorted = path + ".unsorted.bam" + with pysam.AlignmentFile(unsorted, "wb", header=header) as handle: + for read in sorted(out, key=lambda r: r.reference_start): + handle.write(read) + pysam.sort("-o", path, unsorted) + pysam.index(path) + os.remove(unsorted) + return path + + +@pytest.mark.parametrize("groups", [2, 4]) +def test_contig_groups_write_byte_identical_tables(bams, fasta, tmp_path, groups): + """GIVEN a pileup run as one aggregate and as several contig batches + WHEN the written tables are hashed + THEN every Parquet file is byte-for-byte the same. + + Grouping must be a memory optimisation and nothing else. It holds + because batches partition the contigs, and a cut site belongs to + exactly one contig, so no count can straddle a batch boundary.""" + + whole = str(tmp_path / "whole") + split = str(tmp_path / "split") + + one = pileup_pkg.pileup_alignments( + [bams[0]], + fasta, + whole, + unstranded=True, + pos_shift=4, + neg_shift=-4, + contig_groups=1, + ) + many = pileup_pkg.pileup_alignments( + [bams[0]], + fasta, + split, + unstranded=True, + pos_shift=4, + neg_shift=-4, + contig_groups=groups, + ) + + for left, right in zip(one, many): + assert _digest(left) == _digest(right) + assert _digest(left), "table wrote no Parquet files" + assert tables.read_manifest(left)["rows"] == tables.read_manifest(right)["rows"] + + +def test_grouping_tolerates_a_reference_contig_the_bam_never_mentions( + bams, data_dir, tmp_path +): + """GIVEN a reference carrying a contig absent from the BAM header + WHEN the pileup is split into contig batches + THEN it completes and matches the ungrouped run. + + polars-bio raises rather than returning nothing when asked for a + region its header does not name, so batches have to be built from + the intersection. A reference with more contigs than the alignment + is the normal case, not an edge case -- hg38 has 455 where an ATAC + BAM has 195.""" + + rng = random.Random(7) + path = str(tmp_path / "extra.fa") + sizes = dict(CHROM_SIZES) + sizes["chrUnplaced"] = 300 + with open(path, "w") as handle: + for chrom, size in sizes.items(): + handle.write(">{}\n".format(chrom)) + seq = "".join(rng.choice("ACGT") for _ in range(size)) + for i in range(0, size, 60): + handle.write(seq[i : i + 60] + "\n") + pysam.faidx(path) + + whole = pileup_pkg.pileup_alignments( + [bams[0]], path, str(tmp_path / "w"), unstranded=True, contig_groups=1 + ) + split = pileup_pkg.pileup_alignments( + [bams[0]], path, str(tmp_path / "s"), unstranded=True, contig_groups=3 + ) + + assert _digest(whole[0]) == _digest(split[0]) + assert "chrUnplaced.parquet" not in _digest(split[0]) + + +def test_pooled_alignments_with_unlike_headers_keep_every_record(bams, fasta, tmp_path): + """GIVEN one channel pooling a two-contig BAM and a one-contig BAM + WHEN the pileup is split into contig batches + THEN the table matches the ungrouped run. + + Each branch is restricted to the contigs its own table has. Taking + the intersection across the pooled alignments instead would drop + chr2 entirely and still look like a successful run.""" + + solo = _one_contig_bam(str(tmp_path / "solo.bam")) + pooled = [bams[0], solo] + + whole = pileup_pkg.pileup_alignments( + pooled, fasta, str(tmp_path / "w"), unstranded=True, contig_groups=1 + ) + split = pileup_pkg.pileup_alignments( + pooled, fasta, str(tmp_path / "s"), unstranded=True, contig_groups=2 + ) + + assert _digest(whole[0]) == _digest(split[0]) + # chr2 exists only in the first alignment; a naive intersection + # across the pool would have discarded it. + assert "chr2.parquet" in _digest(split[0]) + + +def test_bam_contigs_matches_the_header_pysam_reads(bams): + """GIVEN a BAM + WHEN its header is read with the stdlib rather than pysam + THEN the reference sequences and lengths agree.""" + + with pysam.AlignmentFile(bams[0], "rb") as handle: + expected = dict(zip(handle.references, handle.lengths)) + + assert alignments.bam_contigs(bams[0]) == expected + + +def test_bam_contigs_declines_anything_that_is_not_a_bam(tmp_path): + """GIVEN a SAM path + WHEN its contigs are asked for + THEN None comes back, because SAM carries no index to restrict.""" + + assert alignments.bam_contigs(str(tmp_path / "reads.sam")) is None + + +def test_bam_contigs_declines_a_file_it_cannot_read(tmp_path): + """GIVEN a path that is missing, and one that is not really a BAM + WHEN their contigs are asked for + THEN None comes back rather than an exception. + + Reading the header is an optimisation, not a validation step. The + engine opens the same file moments later and reports the problem + better than a gzip traceback would, and a header that cannot be + read only means the pileup is not split.""" + + junk = tmp_path / "junk.bam" + junk.write_bytes(b"not actually a bam") + + assert alignments.bam_contigs(str(tmp_path / "missing.bam")) is None + assert alignments.bam_contigs(str(junk)) is None + + +### +# Contig naming and the BAM index +# +# Both of these were found against a corpus of deliberately defective +# files rather than against the synthetic BAMs above, which are all +# indexed and all named to match their reference. Each failure used to +# be silent, and the tests here are about the noise. +### + + +@pytest.mark.parametrize("groups", [1, 4]) +def test_a_reference_sharing_no_contig_with_the_alignment_is_refused( + fasta, tmp_path, groups +): + """GIVEN an Ensembl-headered alignment and a UCSC-named reference + WHEN a pileup is requested + THEN it raises rather than writing an empty table. + + Every record would be dropped by the join against the chrom sizes, + leaving a table with no rows that `require_complete` passes, since + a manifest listing no files is one whose files all exist. Training + then reads a genome with no signal in it. Refused at one batch as + well as four, because the empty table predates grouping.""" + + solo = _one_contig_bam(str(tmp_path / "ensembl.bam"), chrom="1") + name = str(tmp_path / "out") + + with pytest.raises(ValueError, match="would write an empty table"): + pileup_pkg.pileup_alignments( + [solo], fasta, name, unstranded=True, contig_groups=groups + ) + + assert not os.path.exists(name + tables.CUT_SITE_SUFFIX) + + +def test_the_refusal_names_the_alignment_and_both_conventions(fasta, tmp_path): + """GIVEN a contig naming mismatch + WHEN the pileup refuses + THEN the message names the file and a contig from either side. + + The cause is almost never a wrong genome, it is a convention, and + the two are told apart by seeing `1` beside `chr1`.""" + + solo = _one_contig_bam(str(tmp_path / "ensembl.bam"), chrom="1") + + with pytest.raises(ValueError) as error: + pileup_pkg.pileup_alignments( + [solo], fasta, str(tmp_path / "out"), unstranded=True + ) + + assert "ensembl.bam" in str(error.value) + assert "chr1" in str(error.value) + + +def test_a_pooled_alignment_sharing_no_contig_is_refused(bams, fasta, tmp_path): + """GIVEN a channel pooling a matching alignment with a mismatched one + WHEN a pileup is requested + THEN it raises rather than counting only the matching one. + + This is the quiet case the check exists for. The other branch keeps + the batches non-empty, so nothing looks wrong: the run succeeds, the + table verifies, and one alignment's records are simply absent.""" + + solo = _one_contig_bam(str(tmp_path / "ensembl.bam"), chrom="1") + + with pytest.raises(ValueError, match="ensembl.bam"): + pileup_pkg.pileup_alignments( + [bams[0], solo], + fasta, + str(tmp_path / "out"), + unstranded=True, + contig_groups=2, + ) + + +def test_an_unreadable_header_is_exempt_from_the_contig_check(fasta, tmp_path): + """GIVEN an alignment that does not exist + WHEN a pileup is requested + THEN the engine reports the open failure, not the contig check. + + Diagnosing an unreadable file belongs to the component that opens + it. Claiming a naming mismatch for a missing BAM would be worse + than saying nothing, and it is what pins `bam_contigs` returning + None rather than raising.""" + + with pytest.raises(Exception) as error: + pileup_pkg.pileup_alignments( + [str(tmp_path / "missing.bam")], + fasta, + str(tmp_path / "out"), + unstranded=True, + ) + + assert "would write an empty table" not in str(error.value) + + +def test_splitting_an_unindexed_alignment_warns_and_still_matches(bams, fasta, tmp_path): + """GIVEN an alignment with no .bai beside it + WHEN it is piled up in several contig batches + THEN a warning says what the scans cost, and the table is unchanged. + + Without an index a contig predicate is still an ordinary filter, so + the rows are identical; it is only no longer free. The warning must + report that and change nothing else.""" + + bare = str(tmp_path / "bare.bam") + shutil.copy(bams[0], bare) + + indexed = pileup_pkg.pileup_alignments( + [bams[0]], fasta, str(tmp_path / "i"), unstranded=True, contig_groups=2 + ) + + with pytest.warns(UserWarning, match="samtools index"): + split = pileup_pkg.pileup_alignments( + [bare], fasta, str(tmp_path / "b"), unstranded=True, contig_groups=2 + ) + + assert _digest(indexed[0]) == _digest(split[0]) + + +def test_an_indexed_alignment_splits_without_warning(bams, fasta, tmp_path): + """GIVEN an alignment with its index beside it + WHEN it is piled up in several contig batches + THEN nothing is warned about, because the batches are nearly free.""" + + with warnings.catch_warnings(): + warnings.simplefilter("error", UserWarning) + pileup_pkg.pileup_alignments( + [bams[0]], fasta, str(tmp_path / "ok"), unstranded=True, contig_groups=2 + ) + + +def test_an_unindexed_alignment_is_quiet_when_it_is_not_split(bams, fasta, tmp_path): + """GIVEN an alignment with no index + WHEN it is piled up as a single batch + THEN nothing is warned about. + + One batch is one scan whether or not an index could have restricted + it, so there is nothing to report and no reason to make the common + case noisy.""" + + bare = str(tmp_path / "bare.bam") + shutil.copy(bams[0], bare) + + with warnings.catch_warnings(): + warnings.simplefilter("error", UserWarning) + pileup_pkg.pileup_alignments( + [bare], fasta, str(tmp_path / "one"), unstranded=True, contig_groups=1 + ) + + +def test_the_index_check_accepts_both_htslib_conventions(bams, tmp_path): + """GIVEN the two index names htslib accepts, and a .csi + WHEN each is tested + THEN both .bai spellings count and the .csi does not. + + polars-bio cannot open a CSI-indexed BAM at all, so treating one as + indexed would promise a pushdown that does not exist.""" + + suffixed = str(tmp_path / "suffixed.bam") + replaced = str(tmp_path / "replaced.bam") + csi_only = str(tmp_path / "csi.bam") + for path in (suffixed, replaced, csi_only): + shutil.copy(bams[0], path) + + shutil.copy(bams[0] + ".bai", suffixed + ".bai") + shutil.copy(bams[0] + ".bai", replaced[: -len(".bam")] + ".bai") + shutil.copy(bams[0] + ".bai", csi_only + ".csi") + + assert alignments._has_bam_index(suffixed) + assert alignments._has_bam_index(replaced) + assert not alignments._has_bam_index(csi_only) + + +def test_pileup_many_should_say_a_deferred_backend_is_not_ported_yet(): + """Test that asking for the wool backend explains rather than denies. + + Given: + A request for the wool backend, which cherimoya offers and this + package has not ported. + When: + pileup_many is called. + Then: + It should raise NotImplementedError naming the backend and a + working alternative, rather than the ValueError an unrecognised + name gets -- a caller migrating a working configuration needs to + know the backend is deferred, not that it never existed. + """ + + # Act & assert + with pytest.raises(NotImplementedError, match="not been ported"): + run.pileup_many([], backend="wool") diff --git a/tests/test_pileup_io.py b/tests/test_pileup_io.py new file mode 100644 index 0000000..0571eb6 --- /dev/null +++ b/tests/test_pileup_io.py @@ -0,0 +1,458 @@ +"""Tests for reading alignments and writing cut-site tables. + +Ported from cherimoya's ``tests/test_giql_io.py``, which held the whole data path in +one module. The names it reached for as ``giql_io.x`` and +``pileup.x`` are spread over several modules here, so the references +are rewritten and nothing else is: the assertions are the evidence +that the split preserved behaviour, and rewriting them in the same +change that moves them would destroy that evidence. + +Style follows cherimoya rather than this project's test conventions -- +natural-language names, no Arrange-Act-Assert phases. Converting them +is a separate change, tracked on the epic. +""" + +import gzip +import os +import random + +import numpy +import pytest + +pytest.importorskip("polars_bio") +pytest.importorskip("polars") +pysam = pytest.importorskip("pysam") + + +from quadrat import _engine, alignments, reference, tables +from quadrat import pileup as pileup_pkg +from quadrat.pileup import sql + +os.environ.setdefault("TQDM_DISABLE", "1") + +CHROM_SIZES = {"chr1": 1000, "chr2": 500} +POS_SHIFT, NEG_SHIFT = 4, -4 +IGNORE = list("QWERYUIOPSDFHJKLZXVBNM") + + +### +# Fixtures +### + + +@pytest.fixture(scope="module") +def data_dir(tmp_path_factory): + return tmp_path_factory.mktemp("giql_io") + + +@pytest.fixture(scope="module") +def fasta(data_dir): + rng = random.Random(0) + path = str(data_dir / "genome.fa") + with open(path, "w") as f: + for chrom, size in CHROM_SIZES.items(): + seq = list(rng.choice("ACGT") for _ in range(size)) + # Both stretches sit inside windows the tests keep: the + # lowercase run under the chr1 800-840 locus, the N run under + # chr1 100-140 (and inside every wide window over chr2 200-260). + seq[790:850] = [c.lower() for c in seq[790:850]] + seq[110:120] = ["N"] * 10 + seq[220:230] = ["N"] * 10 + f.write(">{}\n".format(chrom)) + for i in range(0, size, 60): + f.write("".join(seq[i : i + 60]) + "\n") + return path + + +def _read(name, chrom, pos, cigar, flag, header): + """Build one aligned segment with a dummy query and qualities.""" + + read = pysam.AlignedSegment(header) + read.query_name = name + read.flag = flag + if chrom is not None: + read.reference_id = header.get_tid(chrom) + read.reference_start = pos + read.cigarstring = cigar + else: + read.reference_id = -1 + read.reference_start = -1 + + qlen = read.infer_query_length() or 20 + read.query_sequence = "A" * qlen + read.query_qualities = pysam.qualitystring_to_array("I" * qlen) + read.mapping_quality = 30 + return read + + +def _write_bam(path, reads, header): + unsorted = path + ".unsorted.bam" + with pysam.AlignmentFile(unsorted, "wb", header=header) as out: + for read in reads: + out.write(read) + pysam.sort("-o", path, unsorted) + pysam.index(path) + os.remove(unsorted) + return path + + +@pytest.fixture(scope="module") +def bam_header(): + return pysam.AlignmentHeader.from_dict( + { + "HD": {"VN": "1.6", "SO": "coordinate"}, + "SQ": [ + {"SN": "chr1", "LN": 1000}, + {"SN": "chr2", "LN": 500}, + {"SN": "chrZ", "LN": 800}, + ], + } + ) + + +@pytest.fixture(scope="module") +def bam_pair(data_dir, bam_header): + h = bam_header + first = [ + _read("f1", "chr1", 100, "20M", 0, h), + _read("f1_secondary", "chr1", 100, "20M", 256, h), + _read("f1_duplicate", "chr1", 100, "20M", 1024, h), + _read("r1", "chr1", 150, "20M", 16, h), + _read("f_del", "chr1", 200, "10M5D10M", 0, h), + _read("r_clip", "chr1", 300, "5S15M", 16, h), + _read("r_skip", "chr1", 400, "10M100N10M", 16, h), + _read("placed_unmapped", "chr1", 600, "20M", 4, h), + _read("unmapped", None, None, None, 4, h), + _read("on_chrZ", "chrZ", 50, "20M", 0, h), + _read("c2_f", "chr2", 10, "20M", 0, h), + _read("c2_r", "chr2", 480, "20M", 16, h), + ] + second = [ + _read("f2", "chr1", 700, "20M", 0, h), + _read("r2", "chr1", 100, "20M", 16, h), + _read("c2_f_again", "chr2", 10, "20M", 0, h), + ] + return [ + _write_bam(str(data_dir / "first.bam"), first, h), + _write_bam(str(data_dir / "second.bam"), second, h), + ] + + +@pytest.fixture(scope="module") +def bam_edges(data_dir, bam_header): + h = bam_header + reads = [ + _read("rev_at_origin", "chr1", 0, "3M", 16, h), + _read("fwd_at_end", "chr1", 998, "2M", 0, h), + _read("fwd_inside", "chr1", 990, "2M", 0, h), + ] + return _write_bam(str(data_dir / "edges.bam"), reads, h) + + +@pytest.fixture(scope="module") +def peaks_bed(data_dir): + rows = [ + ("chr2", 200, 260), # ordinary locus on chr2 (also exercises `chroms`) + ("chr1", 100, 140), # ordinary + ("chr1", 20, 40), # window start < 0 -> dropped + ("chr1", 960, 1000), # window end > chrom length -> dropped + ("chr1", 955, 975), # window end == chrom length -> kept (tangermeme >= 1.4) + ("chr1", 690, 720), # touches excluded bin 6 only through the +1 quirk + ("chr1", 800, 840), # clear of the exclusion zone + ("chr1", 930, 940), # ordinary, near the end + ("chr1", 540, 560), # inside the exclusion zone + ] + path = str(data_dir / "peaks.bed") + with open(path, "w") as f: + for chrom, start, end in rows: + f.write("{}\t{}\t{}\tpeak\t0\t.\n".format(chrom, start, end)) + return path + + +@pytest.fixture(scope="module") +def exclusion_bed(data_dir): + path = str(data_dir / "exclusion.bed.gz") + with gzip.open(path, "wt") as f: + f.write("chr1\t500\t600\n") + return path + + +def _oracle_pileup(bam_paths, chrom_sizes, pos_shift, neg_shift, scale=1.0): + """bam2bw's loop, densified: every mapped record on a known contig + contributes its shifted 5' end; out-of-range sites are dropped.""" + + dense = {c: numpy.zeros(n, dtype=numpy.float64) for c, n in chrom_sizes.items()} + for path in bam_paths: + with pysam.AlignmentFile(path, "rb") as bam: + for read in bam.fetch(until_eof=True): + if read.is_unmapped or read.reference_name not in dense: + continue + start = read.reference_start + pos_shift + end = read.reference_end + neg_shift + pos = start if read.is_forward else end - 1 + if 0 <= pos < chrom_sizes[read.reference_name]: + dense[read.reference_name][pos] += 1 + return {c: v * scale for c, v in dense.items()} + + +def _dense_from_parquet(path, chrom_sizes): + import polars + + frame = polars.read_parquet(path) + dense = {c: numpy.zeros(n, dtype=numpy.float64) for c, n in chrom_sizes.items()} + for chrom, pos, value in frame.iter_rows(): + dense[chrom][pos] = value + return dense, frame + + +@pytest.fixture(scope="module") +def cut_sites(data_dir, bam_pair, fasta): + _engine.clear_cache() + return pileup_pkg.pileup_alignments( + bam_pair, + fasta, + str(data_dir / "pair"), + pos_shift=POS_SHIFT, + neg_shift=NEG_SHIFT, + unstranded=True, + ) + + +### +# The polars-bio BAM provider +### + + +def test_bam_provider_coordinates_should_match_pysam(bam_pair): + """GIVEN a BAM with deletions, soft clips and reference skips + WHEN it is read through polars-bio's BAM provider + THEN start/end equal pysam's 0-based reference_start/reference_end, + unmapped records never reach the pileup, and the pinned offset holds.""" + + import polars_bio as pb + + pb.register_bam(bam_pair[0], "test_pin") + frame = ( + pb.sql('SELECT name, chrom, start, "end", flags FROM test_pin') + .collect() + .to_pandas() + .set_index("name") + ) + + with pysam.AlignmentFile(bam_pair[0], "rb") as bam: + for read in bam.fetch(until_eof=True): + if read.is_unmapped: + continue + row = frame.loc[read.query_name] + assert row["chrom"] == read.reference_name + assert ( + int(row["start"]) + alignments._BAM_START_OFFSET == read.reference_start + ), read.query_name + assert ( + int(row["end"]) + alignments._BAM_START_OFFSET == read.reference_end + ), read.query_name + + unmapped = frame[(frame["flags"] & 4) != 0] + if len(unmapped): + # The provider surfaces unmapped rows; the pileup SQL must skip them. + assert {"placed_unmapped", "unmapped"} >= set(unmapped.index) + + +### +# Cut-site pileup +### + + +def test_pileup_alignments_should_match_bam2bw_semantics(cut_sites, bam_pair): + """GIVEN two BAMs with secondary, duplicate, unmapped and off-contig reads + WHEN they are piled up with the ATAC +4/-4 shift, unstranded + THEN every position equals a pysam re-implementation of bam2bw's loop + (all files pooled, only unmapped and unknown-contig reads skipped).""" + + expected = _oracle_pileup(bam_pair, CHROM_SIZES, POS_SHIFT, NEG_SHIFT) + dense, frame = _dense_from_parquet(cut_sites[0], CHROM_SIZES) + + assert cut_sites == [cut_sites[0]] + assert cut_sites[0].endswith(tables.CUT_SITE_SUFFIX) + assert frame.schema["pos"].is_integer() + assert frame.schema["value"].is_float() + assert frame["chrom"].to_list() == sorted(frame["chrom"].to_list()) + for chrom in CHROM_SIZES: + numpy.testing.assert_array_equal(dense[chrom], expected[chrom]) + + # Spot checks that pin the semantics independently of the oracle. + assert dense["chr1"][100 + POS_SHIFT] == 3 # primary + secondary + duplicate + assert dense["chr1"][170 - 1 + NEG_SHIFT] == 1 # reverse read cuts at end - 1 + assert dense["chr1"][520 - 1 + NEG_SHIFT] == 1 # 10M100N10M spans the skip + assert dense["chr1"][315 - 1 + NEG_SHIFT] == 1 # 5S15M: clip is not reference + assert dense["chr2"][10 + POS_SHIFT] == 2 # pooled across files + assert dense["chr1"][600 + POS_SHIFT] == 0 # placed unmapped skipped + assert frame["value"].sum() == 12 # 9 records in file one + 3 in file two + + +def test_pileup_alignments_should_apply_scale_factor(data_dir, bam_pair, fasta): + """GIVEN a scale factor of 0.5 + WHEN the same BAMs are piled up + THEN every value is halved and stays a float.""" + + paths = pileup_pkg.pileup_alignments( + bam_pair, + fasta, + str(data_dir / "scaled"), + pos_shift=POS_SHIFT, + neg_shift=NEG_SHIFT, + unstranded=True, + scale_factor=0.5, + ) + expected = _oracle_pileup(bam_pair, CHROM_SIZES, POS_SHIFT, NEG_SHIFT, 0.5) + dense, _ = _dense_from_parquet(paths[0], CHROM_SIZES) + for chrom in CHROM_SIZES: + numpy.testing.assert_array_equal(dense[chrom], expected[chrom]) + + +def test_pileup_alignments_should_split_strands(data_dir, bam_pair, fasta): + """GIVEN stranded output + WHEN the BAMs are piled up + THEN the + table holds forward cut sites, the - table reverse ones, + and together they sum to the unstranded pileup.""" + + paths = pileup_pkg.pileup_alignments( + bam_pair, + fasta, + str(data_dir / "stranded"), + pos_shift=POS_SHIFT, + neg_shift=NEG_SHIFT, + unstranded=False, + ) + assert paths == [ + str(data_dir / "stranded.+.cuts.parquet"), + str(data_dir / "stranded.-.cuts.parquet"), + ] + + plus, _ = _dense_from_parquet(paths[0], CHROM_SIZES) + minus, _ = _dense_from_parquet(paths[1], CHROM_SIZES) + both = _oracle_pileup(bam_pair, CHROM_SIZES, POS_SHIFT, NEG_SHIFT) + assert plus["chr1"][100 + POS_SHIFT] == 3 and minus["chr1"][104] == 0 + assert minus["chr1"][170 - 1 + NEG_SHIFT] == 1 and plus["chr1"][165] == 0 + for chrom in CHROM_SIZES: + numpy.testing.assert_array_equal(plus[chrom] + minus[chrom], both[chrom]) + + +def test_pileup_alignments_should_drop_out_of_range_sites(data_dir, bam_edges, fasta): + """GIVEN reads whose shifted cut sites fall below 0 or past the end + WHEN they are piled up + THEN only the in-range site survives.""" + + paths = pileup_pkg.pileup_alignments( + [bam_edges], + fasta, + str(data_dir / "edges"), + pos_shift=POS_SHIFT, + neg_shift=NEG_SHIFT, + unstranded=True, + ) + dense, frame = _dense_from_parquet(paths[0], CHROM_SIZES) + assert frame.height == 1 + assert dense["chr1"][990 + POS_SHIFT] == 1 + + +def test_pileup_alignments_should_reject_unsupported_modes(bam_pair, fasta, data_dir): + """GIVEN fragments or read-depth normalization + WHEN a pileup is requested + THEN the engine refuses rather than silently diverging from bam2bw.""" + + with pytest.raises(NotImplementedError): + pileup_pkg.pileup_alignments( + bam_pair, fasta, str(data_dir / "x"), fragments=True + ) + with pytest.raises(NotImplementedError): + pileup_pkg.pileup_alignments( + bam_pair, fasta, str(data_dir / "x"), read_depth=True + ) + + +### +# Locus extraction +### + + +def _reference_extract(fasta, bam_pair, **kwargs): + """tangermeme's extract_loci over the oracle pileup (dict signals).""" + + from tangermeme.io import extract_loci + + dense = _oracle_pileup(bam_pair, CHROM_SIZES, POS_SHIFT, NEG_SHIFT) + dense = {c: v.astype(numpy.float32) for c, v in dense.items()} + return extract_loci(sequences=fasta, signals=[dense], **kwargs) + + +def test_cut_site_contigs_lists_a_directory_from_its_filenames(cut_sites): + """GIVEN a written cut-site table + WHEN its contigs are listed + THEN they are the contigs it holds rows for, and no others. + + `chrZ` is in the BAM header but not in the reference, so no row + survived the pileup and no file was written for it.""" + + assert tables.cut_site_contigs(cut_sites[0]) == {"chr1", "chr2"} + + +def _plan_ancestor(plan, parent, child): + """True when every ``child`` node sits under a ``parent`` node. + + DataFusion prints a physical plan depth first, parents before + children and two spaces of indent per level, so one node is an + ancestor of another exactly when it appears earlier and is less + indented.""" + + def nodes(marker): + return [ + (i, len(line) - len(line.lstrip(" "))) + for i, line in enumerate(plan.splitlines()) + if marker in line + ] + + parents, children = nodes(parent), nodes(child) + if not parents or not children: + return False + return all(any(pi < ci and pd < cd for pi, pd in parents) for ci, cd in children) + + +def test_pileup_should_bound_positions_above_the_aggregate(bam_pair, fasta): + """GIVEN the cut-site pileup query + WHEN polars-bio explains it + THEN the chromosome-sizes join takes the grouped result as its input + rather than one row per read.""" + + import polars + import polars_bio as pb + + tables = alignments.register_alignments(bam_pair) + lengths = reference.chrom_lengths(fasta) + _engine._register_frame( + pb, + _engine._SIZES_TABLE, + polars.DataFrame( + { + "chrom": list(lengths.keys()), + "length": list(lengths.values()), + }, + schema={"chrom": polars.Utf8, "length": polars.Int64}, + ), + ) + + plan = pb.sql("EXPLAIN " + sql.pileup_sql(tables)).collect() + physical = next( + row["plan"] + for row in plan.iter_rows(named=True) + if row["plan_type"] == "physical_plan" + ) + + assert "JoinExec" in physical and "AggregateExec" in physical + + # Above, not below: the join probes the grouped rows rather than one + # per read. Below is what overflowed Arrow's 32-bit string offsets at + # 291,063,148 reads, because the join collects one side whole and + # that side was the reads. + assert _plan_ancestor(physical, "JoinExec", "AggregateExec") + assert not _plan_ancestor(physical, "AggregateExec", "JoinExec")