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"jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [extras] docs = ["sphinx"] @@ -914,4 +913,4 @@ docs = ["sphinx"] [metadata] lock-version = "2.0" python-versions = "^3.8.0" -content-hash = "a087243f9a79748bb28ecff439c2e124c113a6f1d4fc87bc96b75b9c0c62bf7b" +content-hash = "831547b695374f6d2bf06fb308116d18beab45e3cdaab05d542dce02de76578d" diff --git a/pybedlite/overlap_detector.py b/pybedlite/overlap_detector.py index ab08225..3b3a834 100644 --- a/pybedlite/overlap_detector.py +++ b/pybedlite/overlap_detector.py @@ -5,10 +5,10 @@ Examples of Detecting Overlaps ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -.. code-block:: python +. code-block:: python >>> from pybedlite.overlap_detector import Interval, OverlapDetector - >>> detector = OverlapDetector() + >>> detector = OverlapDetector[Interval]() >>> query = Interval("chr1", 2, 20) >>> detector.overlaps_any(query) False @@ -27,6 +27,36 @@ >>> detector.get_overlaps(query) [Interval("chr1", 1, 1), interval("chr1", 3, 10)] + +In many cases, other data types would like to be queried using an overlap detector. In this case, +the :class:`~pybedlite.overlap_detector.ItemizedInterval` can be used as follows: + +. code-block:: python + + >>> from pybedlite.overlap_detector import Interval, ItemizedInterval, OverlapDetector + >>> from typing import cast, List + >>> import attr + >>> @attr.s(frozen=True, auto_attribs=True) + class Gene: + id: str + count: int + >>> detector = OverlapDetector[ItemizedInterval[Gene]]() + >>> query = Interval("chr1", 2, 20) + >>> detector.add(ItemizedInterval("chr1", 1, 100, item=Gene(id="PTEN", count=12))) + >>> detector.overlaps_any(query) + True + >>> intervals: List[ItemizedInterval[Gene]] = detector.get_overlaps(query) + >>> intervals + [ItemizedInterval( + refname='chr1', + start=1, end=100, + item=Gene(id='PTEN', count=12), + negative=False, + name=None + )] + >>> intervals[0].item + Gene(id='PTEN', count=12) + Module Contents ~~~~~~~~~~~~~~~ @@ -41,12 +71,14 @@ import itertools from pathlib import Path from typing import Dict +from typing import Generic from typing import Iterable from typing import Iterator from typing import List from typing import Optional from typing import Set from typing import Type +from typing import TypeVar import attr @@ -178,7 +210,38 @@ def from_ucsc( ) from exception -class OverlapDetector(Iterable[Interval]): +IntervalType = TypeVar("IntervalType", bound=Interval) +"""Type for intervals stored in an OverlapDetector. Must be Interval or a sub-class of Interval.""" + + +Item = TypeVar("Item") +"""Type of the item that is carried along with an `ItemizedInterval`""" + + +@attr.s(frozen=True, auto_attribs=True) +class ItemizedInterval(Interval, Generic[Item]): + """A region mapping to the genome that is 0-based and open-ended. It has the `item` attribute + in addition to the `Interval` attributes, such that non-interval objects may be associated + (and stored alongside) `Interval`s in an `OverlapDetector`. + + Attributes: + refname (str): the refname (or chromosome) + start (int): the 0-based start position + end (int): the 0-based end position (exclusive) + item (Item): The item to store + negative (bool): true if the interval is on the negative strand, false otherwise + name (Optional[str]): an optional name assigned to the interval + """ + + refname: str = attr.ib() + start: int = attr.ib() + end: int = attr.ib() + item: Optional[Item] = None + negative: bool = False + name: Optional[str] = None + + +class OverlapDetector(Iterable[IntervalType], Generic[IntervalType]): """Detects and returns overlaps between a set of genomic regions and another genomic region. Since :class:`~pybedlite.overlap_detector.Interval` objects are used both to populate the @@ -195,13 +258,13 @@ def __init__(self) -> None: # A mapping from the contig/chromosome name to the associated interval tree self._refname_to_tree: Dict[str, cr.cgranges] = {} # type: ignore self._refname_to_indexed: Dict[str, bool] = {} - self._refname_to_intervals: Dict[str, List[Interval]] = {} + self._refname_to_intervals: Dict[str, List[IntervalType]] = {} - def __iter__(self) -> Iterator[Interval]: + def __iter__(self) -> Iterator[IntervalType]: """Iterates over the intervals in the overlap detector.""" return itertools.chain(*self._refname_to_intervals.values()) - def add(self, interval: Interval) -> None: + def add(self, interval: IntervalType) -> None: """Adds an interval to this detector. Args: @@ -226,7 +289,7 @@ def add(self, interval: Interval) -> None: # indexing self._refname_to_indexed[refname] = False - def add_all(self, intervals: Iterable[Interval]) -> None: + def add_all(self, intervals: Iterable[IntervalType]) -> None: """Adds one or more intervals to this detector. Args: @@ -258,7 +321,7 @@ def overlaps_any(self, interval: Interval) -> bool: else: return True - def get_overlaps(self, interval: Interval) -> List[Interval]: + def get_overlaps(self, interval: Interval) -> List[IntervalType]: """Returns any intervals in this detector that overlap the given interval. Args: @@ -274,9 +337,9 @@ def get_overlaps(self, interval: Interval) -> List[Interval]: else: if not self._refname_to_indexed[interval.refname]: tree.index() - ref_intervals: List[Interval] = self._refname_to_intervals[interval.refname] + ref_intervals: List[IntervalType] = self._refname_to_intervals[interval.refname] # NB: only return unique instances of intervals - intervals: Set[Interval] = { + intervals: Set[IntervalType] = { ref_intervals[index] for _, _, index in tree.overlap(interval.refname, interval.start, interval.end) } @@ -284,9 +347,9 @@ def get_overlaps(self, interval: Interval) -> List[Interval]: intervals, key=lambda intv: (intv.start, intv.end, intv.negative, intv.name) ) - def get_enclosing_intervals(self, interval: Interval) -> List[Interval]: + def get_enclosing_intervals(self, interval: Interval) -> List[IntervalType]: """Returns the set of intervals in this detector that wholly enclose the query interval. - i.e. query.start >= target.start and query.end <= target.end. + i.e. `query.start >= target.start and query.end <= target.end`. Args: interval: the query interval @@ -297,9 +360,9 @@ def get_enclosing_intervals(self, interval: Interval) -> List[Interval]: results = self.get_overlaps(interval) return [i for i in results if interval.start >= i.start and interval.end <= i.end] - def get_enclosed(self, interval: Interval) -> List[Interval]: + def get_enclosed(self, interval: Interval) -> List[IntervalType]: """Returns the set of intervals in this detector that are enclosed by the query - interval. I.e. target.start >= query.start and target.end <= query.end. + interval. I.e. `target.start >= query.start and target.end <= query.end`. Args: interval: the query interval @@ -312,14 +375,14 @@ def get_enclosed(self, interval: Interval) -> List[Interval]: return [i for i in results if i.start >= interval.start and i.end <= interval.end] @classmethod - def from_bed(cls, path: Path) -> "OverlapDetector": + def from_bed(cls, path: Path) -> "OverlapDetector[Interval]": """Builds a :class:`~pybedlite.overlap_detector.OverlapDetector` from a BED file. Args: path: the path to the BED file Returns: An overlap detector for the regions in the BED file. """ - detector = OverlapDetector() + detector: OverlapDetector[Interval] = OverlapDetector() for region in BedSource(path): detector.add(Interval.from_bedrecord(region)) diff --git a/pybedlite/tests/test_overlap_detector.py b/pybedlite/tests/test_overlap_detector.py index ce27b1e..9460ce5 100644 --- a/pybedlite/tests/test_overlap_detector.py +++ b/pybedlite/tests/test_overlap_detector.py @@ -2,16 +2,18 @@ from typing import List +import attr import pytest from pybedlite.bed_record import BedRecord from pybedlite.bed_record import BedStrand from pybedlite.overlap_detector import Interval +from pybedlite.overlap_detector import ItemizedInterval from pybedlite.overlap_detector import OverlapDetector def run_test(targets: List[Interval], query: Interval, results: List[Interval]) -> None: - detector = OverlapDetector() + detector = OverlapDetector[Interval]() # Use add_all() to covert itself and add() detector.add_all(intervals=targets) # Test overlaps_any() @@ -115,7 +117,7 @@ def test_get_enclosing_intervals() -> None: d = Interval("1", 15, 19) e = Interval("1", 16, 20) - detector = OverlapDetector() + detector = OverlapDetector[Interval]() detector.add_all([a, b, c, d, e]) assert detector.get_enclosing_intervals(Interval("1", 10, 100)) == [a] @@ -130,7 +132,7 @@ def test_get_enclosed() -> None: c = Interval("1", 18, 19) d = Interval("1", 50, 99) - detector = OverlapDetector() + detector = OverlapDetector[Interval]() detector.add_all([a, b, c, d]) assert detector.get_enclosed(Interval("1", 1, 250)) == [a, b, c, d] @@ -147,7 +149,7 @@ def test_iterable() -> None: d = Interval("1", 15, 19) e = Interval("1", 16, 20) - detector = OverlapDetector() + detector = OverlapDetector[Interval]() detector.add_all([a]) assert list(detector) == [a] detector.add_all([a, b, c, d, e]) @@ -208,7 +210,7 @@ def test_construction_from_ucsc_with_strand(strand: str) -> None: `Interval.from_ucsc()` should correctly parse UCSC position-formatted strings with strands. """ expected_interval = Interval("chr1", 100, 200, negative=(strand == "-")) - assert Interval.from_ucsc(f"chr1:101-200({strand})") == expected_interval + assert Interval.from_ucsc(f"chr1:101-200({strand})") == expected_interval # noqa: E231 @pytest.mark.parametrize( @@ -218,4 +220,20 @@ def test_construction_from_ucsc_other_contigs(contig: str) -> None: """ `Interval.from_ucsc()` should accomodate non-human, decoy, custom, and other contig names. """ - assert Interval.from_ucsc(f"{contig}:101-200") == Interval(contig, 100, 200) + assert Interval.from_ucsc(f"{contig}:101-200") == Interval(contig, 100, 200) # noqa: E231 + + +@attr.s(frozen=True, auto_attribs=True) +class Gene: + id: str + count: int + + +def test_itemized_interval() -> None: + detector = OverlapDetector[ItemizedInterval[Gene]]() + query = Interval("chr1", 2, 20) + detector.add(ItemizedInterval("chr1", 1, 100, item=Gene(id="PTEN", count=12))) + print(detector.overlaps_any(query)) + intervals: List[ItemizedInterval[Gene]] = detector.get_overlaps(query) + print(intervals) + print(intervals[0].item) diff --git a/pyproject.toml b/pyproject.toml index 0c1e487..54514f4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,7 +34,7 @@ sphinx = { version = "^7.0.0", optional = true } [tool.poetry.dev-dependencies] pytest = "^7.0.0" -mypy = "^1.5.0" +mypy = "^1.10.1" flake8 = "^5.0.0" black = "^23.0.0" isort = "^5.13.0"