Does anyone have a working version of the nested containment list for Python?

Question

[endrebak]

I am interested in using the nested containment list described in https://www.ncbi.nlm.nih.gov/pubmed/17234640

but the version in the github repo https://github.com/cjlee112/pygr does not seem to build properly. Does anyone have an example project that uses the nested containment list?

[endrebak]

I was able to update it for cython so the installation runs smoothly, but I am still unable to run it. Is it really better or was it just better than the intervaltree implementations back in 2009?

[h.mon]

Which version of python are you using? The code is really old - from 2011 - and mentions as requirement "Python >= 2.3", among others. I guess it bit-rotted. Try to use old versions of the requirements packages, you may even have to use some older python version.

edit: by the way, use virtualenv to manage these old, potentially conflicting old packages.

[endrebak]

I was able to get it to compile with cython https://github.com/endrebak/pygr

Still cannot get it to work though. Will rather try to write a new wrapper for the C API.

Thanks.

[endrebak]

Wow it is fast! Uses about 1/240 of the time to build the structure, even compared to https://github.com/biocore-ntnu/kerneltree !!! Will push a Python wrapper soon.