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
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 0.3.8
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
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|---|---|---|---|---|
| GenomicRanges-0.3.8-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 96.1 kB
Release files / GenomicRanges-0.3.8.tar.gz
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