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.
Note: V0.4.0 is a complete overhaul of the package, as such the constructor to GenomicRanges has changed!
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 ...
from IRanges (Preferred way)
If you have all relevant information to create a GenomicRanges object
from genomicranges import GenomicRanges
from iranges import IRanges
from biocframe import BiocFrame
from random import random
gr = GenomicRanges(
seqnames=[
"chr1",
"chr2",
"chr3",
"chr2",
"chr3",
],
ranges=IRanges(start=[x for x in range(101, 106)], width=[11, 21, 25, 30, 5]),
strand=["*", "-", "*", "+", "-"],
mcols=BiocFrame(
{
"score": range(0, 5),
"GC": [random() for _ in range(5)],
}
),
)
print(gr)
## output
GenomicRanges with 5 ranges and 5 metadata columns
seqnames ranges strand score GC
<str> <IRanges> <ndarray[int64]> <range> <list>
[0] chr1 101 - 112 * | 0 0.2593301003406461
[1] chr2 102 - 123 - | 1 0.7207993213776644
[2] chr3 103 - 128 * | 2 0.23391468067222065
[3] chr2 104 - 134 + | 3 0.7671026589720187
[4] chr3 105 - 110 - | 4 0.03355777784472458
------
seqinfo(3 sequences): chr1 chr2 chr3
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 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 ranges and 5 metadata columns
seqnames ranges strand score GC
<str> <IRanges> <ndarray[int64]> <list> <list>
0 chr1 101 - 112 * | 0 0.4862658925128007
1 chr2 102 - 103 - | 1 0.27948386889389953
2 chr1 103 - 128 * | 2 0.5162697718607901
3 chr3 104 - 134 + | 3 0.5979843806415466
4 chr2 109 - 111 - | 4 0.04740781186083798
------
seqinfo(3 sequences): chr1 chr2 chr3
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, ignore_strand=True)
print(hits)
## output
[[0, 1], [1677082, 1677083, 1677084], [1003411, 1003412]]
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"],
ranges=IRanges([1, 3, 2, 4], [10, 30, 50, 60]),
strand=["-", "+", "*", "+"],
mcols=BiocFrame({"score": [1, 2, 3, 4]}),
)
gr2 = GenomicRanges(
seqnames=["chr2", "chr4", "chr5"],
ranges=IRanges([3, 6, 4], [30, 50, 60]),
strand=["-", "+", "*"],
mcols=BiocFrame({"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 ranges and 4 metadata columns
seqnames ranges strand score
<str> <IRanges> <ndarray> <list>
[0] chr1 1 - 11 - | 1
[1] chr2 3 - 33 + | 2
[2] chr1 2 - 52 * | 3
[3] chr3 4 - 64 + | 4
------
seqinfo(3 sequences): chr1 chr2 chr3
Name: gene2
GenomicRanges with 3 ranges and 3 metadata columns
seqnames ranges strand score
<str> <IRanges> <ndarray> <list>
[0] chr2 3 - 33 - | 2
[1] chr4 6 - 56 + | 3
[2] chr5 4 - 64 * | 4
------
seqinfo(3 sequences): chr2 chr4 chr5
Further information
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 0.4.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| GenomicRanges-0.4.1.tar.gz | 57.9 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| GenomicRanges-0.4.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 89.8 kB
Release files / GenomicRanges-0.4.1.tar.gz
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