User: endrebak
endrebak • 690
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Posts by endrebak
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... Okay, thanks. I am not that interested in the actual way of doing it, I was just wondering if it was possible without hand rolling a solution. It seems like most genomicranges operations are set-like. ...
written 7 months ago by
endrebak • 690
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... In bedtools intersect means "for each read in A, for each read in B that overlaps, find the part of A that overlaps with a read in B".
So that if you have 4 reads in A and 6 reads in B and all overlap you get 4*6 results.
GenomicRanges intersect works differently; for both A and B it first cluste ...
written 8 months ago by
endrebak • 690
• updated
7 months ago by
bruce.moran • 500
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... The fastest implementation in Python I have found in is the Nested Containment List. It is several times faster than the ultrafast intervaltrees found in the kernel. pygr has died from bitrot, but I have revived the underlying datastructure here: https://github.com/hunt-genes/ncls
This datastructur ...
written 9 months ago by
endrebak • 690
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... You now can: https://github.com/endrebak/pyranges
It is still in pre-alpha, but will be updated by me as I use it all the time. ...
written 9 months ago by
endrebak • 690
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... BioRanges was never finished and I have seen no timings. PyRanges seems to be reaching feature parity with GenomicRanges soon. The greatest difference is perhaps that I try to make a dinky convenient wrapper around pandas dfs so that all the good stuff from GenomicRanges can be used on dfs while sti ...
written 9 months ago by
endrebak • 690
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... GenomicRanges for Python.
This library tries to be a thin, but extremely useful wrapper around genomic data contained in pandas dataframes. This allows for all the wonderful functionality of bedtools/bedops and/or GenomicRanges, while being able to use the the enormous universe of Python datascienc ...
written 9 months ago by
endrebak • 690
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... https://github.com/bedops/bedops/blob/master/applications/bed/closestfeats/src/ClosestFeature.cpp Thanks. Iff sorting is much faster than KD-tree construction, I'll try to use your method (I suspect it'll be the other way around though). ...
written 9 months ago by
endrebak • 690
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... Brilliant. There is both a scipy implementation: https://docs.scipy.org/doc/scipy-0.15.1/reference/generated/scipy.spatial.KDTree.html#scipy.spatial.KDTree and a C library that seems like it'll be easy to wrap: https://github.com/jtsiomb/kdtree ...
written 9 months ago by
endrebak • 690
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... Agreed. Sorry about that. ...
written 9 months ago by
endrebak • 690
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... https://github.com/hunt-genes/ncls ...
written 9 months ago by
endrebak • 690
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