genomeblocks.bedpe

Table of contents

1. Pair
2. read_bedpe(filename, *, min_score=None, max_distance=None, verbose=True) -> list[Pair]
3. pair_to_bed(loci, bedpe, *, r=0, either=True, both=False, min_score=None, max_distance=None, verbose=True) -> list[Pair]
4. pairs_to_frame(pairs) -> pandas.DataFrame
5. pairs_to_bedpe(pairs, filename) -> None

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Pair

@dataclass
class Pair:
    chrom1: str; start1: int; end1: int
    chrom2: str; start2: int; end2: int
    name: str = ""
    score: float = 0.0
    strand1: str = "."
    strand2: str = "."
    extra_fields: tuple = ()

    # properties
    mid1 -> int        # (start1 + end1) // 2
    mid2 -> int        # (start2 + end2) // 2
    distance -> int    # |mid2 - mid1| for intra-chrom; float('inf') otherwise

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read_bedpe(filename, *, min_score=None, max_distance=None, verbose=True) -> list[Pair]

Parser. Filters applied in-read if provided.

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pair_to_bed(loci, bedpe, *, r=0, either=True, both=False, min_score=None, max_distance=None, verbose=True) -> list[Pair]

Equivalent to bedtools pairtoBed. Also attached as Loci.pair_to_bed(...).

Arguments:

Arg	Meaning
loci	Loci (or single Locus) to intersect against.
bedpe	Path to a BEDPE file or a pre-loaded list[Pair].
r	Slop radius per anchor before the overlap test.
either	Keep pair if ≥ 1 anchor overlaps (default True).
both	Require both anchors overlap (default False).
min_score, max_distance	In-read filters (passed to read_bedpe).

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pairs_to_frame(pairs) -> pandas.DataFrame

Columns: chrom1, start1, end1, chrom2, start2, end2, name, score, strand1, strand2.

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pairs_to_bedpe(pairs, filename) -> None

Writes TSV BEDPE (10 or more columns when extra_fields is set).