GenomicRanges 0.3.9

Container class to represent and operate over genomic regions and annotations.

GenomicRanges

GenomicRanges provides container classes designed to represent genomic locations and support genomic analysis. It is similar to Bioconductor's GenomicRanges.

Intervals are inclusive on both ends and starts at 1.

To get started, install the package from PyPI

pip install genomicranges

GenomicRanges

GenomicRanges is the base class to represent and operate over genomic regions and annotations.

From UCSC or GTF file

You can easily download and parse genome annotations from UCSC or load a genome annotation from a GTF file,

import genomicranges

gr = genomicranges.read_gtf(<PATH TO GTF>)
# OR
gr = genomicranges.read_ucsc(genome="hg19")

print(gr)
## output
## GenomicRanges with 1760959 intervals & 10 metadata columns.
## ... truncating the console print ...

Pandas DataFrame

A common representation in Python is a pandas DataFrame for all tabular datasets. DataFrame must contain columns "seqnames", "starts", and "ends" to represent genomic intervals. Here's an example:

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.from_pandas(df)
print(gr)

## output
GenomicRanges with 5 intervals & 2 metadata columns
┏━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┓
┃ row_names ┃ seqnames <list> ┃ starts <list> ┃ ends <list> ┃ strand <list> ┃ score <list> ┃ GC <list>           ┃
┡━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━┩
│ 0         │ chr1            │ 101           │ 112         │ *             │ 0            │ 0.22617584001235103 │
│ 1         │ chr2            │ 102           │ 103         │ -             │ 1            │ 0.25464256182466394 │
│ ...       │ ...             │ ...           │ ...         │ ...           │ ...          │ ...                 │
│ 4         │ chr2            │ 109           │ 111         │ -             │ 4            │ 0.5414168889911801  │
└───────────┴─────────────────┴───────────────┴─────────────┴───────────────┴──────────────┴─────────────────────┘

Interval Operations

GenomicRanges supports most interval based operations.

subject = genomicranges.from_ucsc(genome="hg38")

query = genomicranges.from_pandas(
    pd.DataFrame(
        {
            "seqnames": ["chr1", "chr2", "chr3"],
            "starts": [100, 115, 119],
            "ends": [103, 116, 120],
        }
    )
)

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

GenomicRangesList

Just as it sounds, a GenomicRangesList is a named-list like object. If you are wondering why you need this class, a GenomicRanges object lets us specify multiple genomic elements, usually where the genes start and end. Genes are themselves made of many sub-regions, e.g. exons. GenomicRangesList allows us to represent this nested structure.

Currently, this class is limited in functionality.

To construct a GenomicRangesList

gr1 = GenomicRanges(
    {
        "seqnames": ["chr1", "chr2", "chr1", "chr3"],
        "starts": [1, 3, 2, 4],
        "ends": [10, 30, 50, 60],
        "strand": ["-", "+", "*", "+"],
        "score": [1, 2, 3, 4],
    }
)

gr2 = GenomicRanges(
    {
        "seqnames": ["chr2", "chr4", "chr5"],
        "starts": [3, 6, 4],
        "ends": [30, 50, 60],
        "strand": ["-", "+", "*"],
        "score": [2, 3, 4],
    }
)

grl = GenomicRangesList(ranges=[gr1, gr2], names=["gene1", "gene2"])
print(grl)

## output
GenomicRangesList with 2 genomic elements

Name: gene1
            GenomicRanges with 4 intervals & 1 metadata columns
┏━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓
┃ seqnames <list> ┃ starts <list> ┃ ends <list> ┃ strand <list> ┃ score <list> ┃
┡━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━┩
│ chr1            │ 1             │ 10          │ -             │ 1            │
│ chr2            │ 3             │ 30          │ +             │ 2            │
│ chr3            │ 4             │ 60          │ +             │ 4            │
└─────────────────┴───────────────┴─────────────┴───────────────┴──────────────┘

Name: gene2
            GenomicRanges with 3 intervals & 1 metadata columns
┏━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓
┃ seqnames <list> ┃ starts <list> ┃ ends <list> ┃ strand <list> ┃ score <list> ┃
┡━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━┩
│ chr2            │ 3             │ 30          │ -             │ 2            │
│ chr4            │ 6             │ 50          │ +             │ 3            │
│ chr5            │ 4             │ 60          │ *             │ 4            │
└─────────────────┴───────────────┴─────────────┴───────────────┴──────────────┘

Further information

• Tutorial
• API documentation
• Bioc/GenomicRanges

Note

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