dolomite-ranges 0.4.0

Stage and load genomic ranges from disk.

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/.