GenomicRanges

Python equivalent to Bioconductor's GenomicRanges to represent genomic locations and support genomic analysis. It uses efficient structures already available in the Python/Pandas/numpy eco-system adds an familiar interfaces.

Install

Package is deployed to PyPI

pip install genomicranges

Usage

The package provide several ways to represent genomic intervals

Pandas DataFrame

A common representation in Python is a pandas DataFrame for all tabular datasets. One can convert this into GenomicRanges.

Note: The DataFrame must contain columns seqname, start and end that represent chromosome and genomic coordinates.

from genomicranges import GenomicRanges

gr = GenomicRanges.fromPandas(<PANDAS DATA FRAME>)

From UCSC or GTF file

Methods are available to easily access UCSC genomes or load a genome annotation from GTF

from genomicranges import GenomicRanges

gr = GenomicRanges.fromGTF(<PATH TO GTF>)
# OR 
gr = GenomicRanges.fromUCSC(genome="hg19")

Interval Operations

Currently supports Nearest Genomic positions operation in Bioconductor, but more coming soon.

subject = GenomicRanges.fromUCSC(genome="hg38")

query = GenomicRanges.fromPandas(
    pd.DataFrame(
        {
            "seqname": ["chr1", "chr2", "chr3"],
            "start": [100, 115, 119],
            "end": [103, 116, 120],
        }
    )
)

hits = subject.nearest(query)
print(hits)

Note

This project has been set up using PyScaffold 4.1.1. For details and usage information on PyScaffold see https://pyscaffold.org/.

Release files for genomicranges 0.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for genomicranges 0.1
File	Size	Uploaded
GenomicRanges-0.1.tar.gz	22.8 kB	Jun 14, 2022	Details

Built distribution (wheel)

Table of built distributions (wheels) for genomicranges 0.1
File	Interpreter	ABI	Platform	Reset
GenomicRanges-0.1-py3-none-any.whl 7.9 kB Jun 14, 2022	Python 3	none	any	Details

Total release size: 30.7 kB

Release files / GenomicRanges-0.1.tar.gz

Download URL	GenomicRanges-0.1.tar.gz
Size	22.8 kB
Tags	Source
SHA-256 checksum How to use checksums	`1664dc95b8824eafa877b11699aa158a38fcbd9bc9d0058b196f128b69323a23`
BLAKE2b-256 checksum How to use checksums	`f8983e3203fd5e657991befa44e2dea23ec2df2c2b5573af9accdd3ddb7672b1`
Upload date	Jun 14, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.1 CPython/3.9.13`

Release files / GenomicRanges-0.1-py3-none-any.whl

Download URL	GenomicRanges-0.1-py3-none-any.whl
Size	7.9 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`40f7e5aa6bef86c0785369251d52dc34f8f9d5df5d64633b15eb097454254178`
BLAKE2b-256 checksum How to use checksums	`09b166124bd9f9466a6670dd49719d48f75e2c8ee39ee62b845fe2281dd5129c`
Upload date	Jun 14, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.1 CPython/3.9.13`