pyranges

library0.1.4pypypi✓ verified 86d ago

PyRanges is a Python library for representing and analyzing genomic intervals, similar to Bioconductor's GenomicRanges. It provides efficient operations for overlap, merging, and annotation of genomic ranges. Version 0.1.4 is current; release cadence is irregular.

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pip install pyranges

github ↗homepage ↗

INSTALL

IMPORT

SIG · PYRANGES

pyranges

analyticspythonv0.1.4

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

PyRanges

✓ from pyranges import PyRanges

✗ import pyranges as pr

Common mistake: importing the module then trying to use pr.PyRanges works, but the correct class import is from pyranges import PyRanges

Create a PyRanges object from a pandas DataFrame.

import pandas as pd from pyranges import PyRanges df = pd.DataFrame({ 'Chromosome': ['chr1', 'chr1', 'chr2'], 'Start': [100, 200, 300], 'End': [150, 250, 400] }) gr = PyRanges(df) print(gr)

Debug

Known issues

gotchaPyRanges expects 0-based, half-open intervals (Start inclusive, End exclusive). Using 1-based coordinates will cause off-by-one errors in overlaps.

fix

Always use 0-based, half-open intervals.

affects: all

gotchaThe Chromosome column must be a string, not an integer. If you supply integers, overlaps may fail silently.

fix

Ensure Chromosome column is of dtype str.

affects: all

gotchaStrand information is supported only if a column named 'Strand' exists with values '+', '-', or '.'. Missing or invalid Strand causes errors in strand-specific operations.

fix

Include a Strand column with correct values when needed.

affects: all

Errors

Common errors & fixes

AttributeError: module 'pyranges' has no attribute 'PyRanges'

Imported the module instead of the class.

fix

Use 'from pyranges import PyRanges' then 'PyRanges(...)'.

ValueError: Chromosome column not found

DataFrame missing required column 'Chromosome'.

fix

Ensure DataFrame has columns: Chromosome, Start, End.

ValueError: Start column not found

DataFrame missing required column 'Start'.

fix

Include 'Start' column with integer values.

Upgrade

Version history

0.1.4latest on PyPI · released Mar 14, 2025

Audit

Dependencies

pandasrequiredCore data structure for genomic intervals

numpyrequiredNumerical computing support

nclsrequiredInterval tree data structure

Agent activity

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OpenAI (training)

Resources

githubhttp://github.com/pyranges/pyranges ↗

homepagehttp://github.com/pyranges/pyranges ↗