GenomicRanges

Container class to represent genomic locations and support genomic analysis in Python similar to Bioconductor's GenomicRanges.

Install

Package is published to PyPI

pip install genomicranges

Usage

The package provide several ways to represent genomic annotations and intervals.

Initialize a `GenomicRanges` object

Pandas DataFrame

A common representation in Python is a pandas DataFrame for all tabular datasets. One can convert this into GenomicRanges. Intervals are inclusive on both ends.

Note: The DataFrame must contain columns seqnames, starts and ends to represent genomic coordinates.

from genomicranges import GenomicRanges
import pandas as pd

df = pd.DataFrame(
    {
        "seqnames": ["chr1", "chr2", "chr1", "chr3", "chr2"],
        "starts": [101, 102, 103, 104, 109],
        "ends": [112, 103, 128, 134, 111],
        "strand": ["*", "-", "*", "+", "-"],
        "score": range(0, 5),
        "GC": [random() for _ in range(5)],
    }
)

gr = GenomicRanges.fromPandas(df)

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 most commonly used interval based operations.

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)

Checkout the documentation for more usecases.

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 0.2

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 0.2
File	Size	Uploaded
GenomicRanges-0.2.tar.gz	43.9 kB	Dec 13, 2022	Details

Built distribution (wheel)

Table of built distributions (wheels) for genomicranges 0.2
File	Interpreter	ABI	Platform	Reset
GenomicRanges-0.2-py3-none-any.whl 22.9 kB Dec 13, 2022	Python 3	none	any	Details

Total release size: 66.8 kB

Release files / GenomicRanges-0.2.tar.gz

Download URL	GenomicRanges-0.2.tar.gz
Size	43.9 kB
Tags	Source
SHA-256 checksum How to use checksums	`74c3ebd7491f4745e846ef842ea4402715ec4e1fcdefc937e89bb62e54814d07`
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Upload date	Dec 13, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`

Release files / GenomicRanges-0.2-py3-none-any.whl

Download URL	GenomicRanges-0.2-py3-none-any.whl
Size	22.9 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`80b73fa2e4ecdb5d8cbb7f9d4e1f69afdb7f2f444c598a44a0d311249e8cc82c`
BLAKE2b-256 checksum How to use checksums	`7706ecbbfbbf9c95a2c5b94e87deceae9f4ab0bb5fd6b6719c0ba734b038fa82`
Upload date	Dec 13, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.9.16`