Save and load genomic ranges objects to file

This package implements methods for saving and loading GenomicRanges and GenomicRangesList objects. It provides a language-agnostic method for serializing genomic coordinates in these objects, as well as data in related objects like sequence information. To get started, install the package from PyPI:

pip install dolomite-ranges

We can then save a GenomicRanges to a file, preserving its metadata and mcols:

import os
from tempfile import mkdtemp

from dolomite_base import read_object, save_object
from genomicranges import GenomicRanges
from iranges import IRanges
import dolomite_ranges

gr = GenomicRanges(
     seqnames=["chrA", "chrB", "chrC"],
     ranges=IRanges([10, 30, 2200], [20, 50, 30]),
     strand=["*", "+", "-"],
)

dir = os.path.join(mkdtemp(), "granges")
save_object(gr, dir)

roundtrip = read_object(dir)

Similarly save and load a GenomicRangesList to a file,

import os
from tempfile import mkdtemp

from dolomite_base import read_object, save_object
from genomicranges import GenomicRanges, SeqInfo
from iranges import IRanges
import dolomite_ranges

a = GenomicRanges(
     seqnames=["chr1", "chr2", "chr1", "chr3"],
     ranges=IRanges([1, 3, 2, 4], [10, 30, 50, 60]),
     strand=["-", "+", "*", "+"],
     mcols=BiocFrame({"score": [1, 2, 3, 4]}),
)

b = GenomicRanges(
     seqnames=["chr2", "chr4", "chr5"],
     ranges=IRanges([3, 6, 4], [30, 50, 60]),
     strand=["-", "+", "*"],
     mcols=BiocFrame({"score": [2, 3, 4]}),
)

grl = GenomicRangesList(ranges=[a, b], names=["a", "b"])

dir = os.path.join(mkdtemp(), "granges_list")
save_object(gr, dir)

roundtrip = read_object(dir)

Note

This project has been set up using PyScaffold 4.5. For details and usage information on PyScaffold see https://pyscaffold.org/.