genomeblocks.loci

Table of contents

1. Loci(list)
   1. Construction
   2. Properties
   3. Set-algebra operators
   4. Methods
   5. Conversion
   6. Attached methods (from other modules)
   7. Indexing
   8. Pickling

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Loci(list)

List subclass of Locus intervals with interval algebra and cached indexes.

Construction

Loci(iterable=(), *, filename=None)         # bare constructor
Loci.make(filename, filetype=None)          # parse a BED / narrowPeak file

File types auto-detected from extension:

• .narrowPeak → BED6+N (columns 1..3 required; col 6 used for strand if present).
• anything else → BED-ish (tab-separated; chrom, start, end, optional strand col 6).

Properties

Name	Description
cgr	Lazy cgranges interval tree.
uids	Lazy {uid → index} dict.

Set-algebra operators

Operator	Method	Semantics
a & b	a.intersect(b)	Loci in a overlapping any b.
a - b	a.difference(b)	Loci in a not overlapping any b.
a / b	a.difference(b)	Alias for -.
a + b	concat	Like Loci([*a, *b]).
a \| b	concat	Same as +.
a ^ b	(a-b) + (b-a)	Symmetric difference.

Methods

Loci.overlaps(key, start=None, end=None)     # key is chrom str or Locus
Loci.slop(n)                                  # expand ±n bp
Loci.sort()                                   # by (chrom, start)
Loci.merge()                                  # collapse overlapping / bookended
Loci.nearest(other, s_names=None, o_names=None)  # → pandas.DataFrame (pyranges)
Loci.subloci(uids: list[str])                 # subset by UID list
Loci.map(other)                                # {a_uid: [b_uid, ...]}
Loci.copy()                                    # shallow copy preserving filename

Conversion

Loci.to_frame(names=None)     # pandas.DataFrame (Chr, Start, End, Strand, Name)
Loci.to_pyranges(names=None)  # pyranges.PyRanges
Loci.to_bed(path=None)        # write BED6 ('\t' separated) to path

Attached methods (from other modules)

Source module	Method
signal	Loci.signal(bigwigs, ...), Loci.plot_heatmap(...), Loci.plot_profiles(...)
motifs	Loci.scan_motifs(genome, motif_path, ...)
bedpe	Loci.pair_to_bed(bedpe, ...)

See the individual module pages for signatures.

Indexing

loci[0]                  # int → Locus
loci[1:5]                # slice → Loci
loci["chr1:100-500(.)"]  # str  → Locus (UID lookup, O(1))

Pickling

__getstate__ / __setstate__ drop the cached _cgr index so pickles don’t leak stale trees.