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(
        {
            "seqnames": ["chr1", "chr2", "chr3"],
            "starts": [100, 115, 119],
            "ends": [103, 116, 120],
        }
    )
)

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

For more use cases, checkout the documentation

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 0.1.1

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 0.1.1
File	Size	Uploaded
GenomicRanges-0.1.1.tar.gz	23.3 kB	Jun 15, 2022	Details

Built distribution (wheel)

Table of built distributions (wheels) for genomicranges 0.1.1
File	Interpreter	ABI	Platform	Reset
GenomicRanges-0.1.1-py3-none-any.whl 8.3 kB Jun 15, 2022	Python 3	none	any	Details

Total release size: 31.6 kB

Release files / GenomicRanges-0.1.1.tar.gz

Download URL	GenomicRanges-0.1.1.tar.gz
Size	23.3 kB
Tags	Source
SHA-256 checksum How to use checksums	`0c7d7dee1b5c56702d610f245f23c4bf79160769f00f76b794112fd1cc62d6d1`
BLAKE2b-256 checksum How to use checksums	`fbc173d2c384b0610a85e7024ba57860f4053dcf882b721f75bd4bbc880d1b7a`
Upload date	Jun 15, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.1 CPython/3.9.13`

Release files / GenomicRanges-0.1.1-py3-none-any.whl

Download URL	GenomicRanges-0.1.1-py3-none-any.whl
Size	8.3 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`da75f2904909631d0751558dd0c7ffadba8be4365fdbfed3edc6dce8580ab817`
BLAKE2b-256 checksum How to use checksums	`31298def5a85d78239bc4ece55984934faf89c0e0fa3afe7eddae7e83603d101`
Upload date	Jun 15, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.1 CPython/3.9.13`