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What Is The Best Library For Handling Interval Logic?

What libraries are there for handling logic on intervals? I really want all the set operations on the intervals at genome scale. Bonus points if it has some persistence mechanism and can track the ancestor of an operation (i.e. interval X is the result of the intersection of Y and Z).

I looked at bx python, but the documentation is not great.

library
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updated by endrebak endrebak • written by Casbon • Casbon

3 answers

Have you tried the bioconductor packages IRanges or GenomicRanges. I have used IRanges earlier for a similar task as suggested by Jeremy.

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updated by Ram Ram • written by Khader Shameer Khader Shameer

Looks pretty good, but how does persistence work with the ranges, or do you need to manually convert each time?

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written by Casbon • Casbon

I don't think the IRanges objects track their own derivation history.

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written by David Quigley David Quigley

@Casbon: +1 David. Not sure about the persistence mechanism.

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written by Khader Shameer Khader Shameer

you can save an IRanges object using... save() Thumbs up for the most advanced interval library at present.

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written by Michael Dondrup Michael Dondrup

Ryan Dale recently released a Python wrapper for BEDtools called pybedtools. BEDTools supports all common genome arithmetic (intersect, merge, complement, join, subtract, etc.) and the Python wrapper would make it relatively simple for you to define a derivation history for the result of each operation.

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written by Aaronquinlan Aaronquinlan

I am partial to https://github.com/biocore-ntnu/pyranges

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written by endrebak endrebak

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