Long running then return an empty list (Python version)

aidenlab / straw

Extract data quickly from Juicebox via straw

MIT License

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Long running then return an empty list (Python version) #68

Closed Nanguage closed 3 years ago

Nanguage commented 3 years ago

Describe the bug The straw python package can't fetch data correctly, when running:

result = matrixObj.getDataFromBinRegion(4000000,6000000,4000000,6000000)

It will be blocked for a monment, then return an empty list.

To Reproduce see the Screenshot. My test data can be downloaded from here.

Expected behavior Return list with readed values.

Screenshots

Desktop (please complete the following information):

OS: Windows 10, WSL2, Ubuntu 20.10
Python version: 3.9.5

sa501428 commented 3 years ago

The Bin coordinates (in getDataFromBinRegion) are defined as genomic_position/resolution, so the issue here will likely be resolved after fixing those coordinates. Alternatively, you may want to use strawC, which is faster, can be installed from the pybind11 folder, and supports the old usage syntax.

Nanguage commented 3 years ago

Thanks for your reply. I will try to use strawC.