Closed sergpolly closed 5 years ago
finally cool2RangeCisPercent.py is added and tested - check out the jupyter notebook: https://nbviewer.jupyter.org/github/dekkerlab/digest-Hi-C/blob/master/cisRangePercent.ipynb
I tried to keep the same interface as the corresponding hdf2RangeCisPercent.py - so this should be plug replaceable ...
hdf2RangeCisPercent.py
basically it does now exactly what Tyler's script was doing just using the streaming pixels approach from cooler - i.e. without ever dumping the whole dense matrix, just like here https://github.com/mirnylab/cooltools/blob/master/cooltools/coverage.py
so given the same input the results are going to be the same ...
problem is though, that cooler balances contact mao differently and it's hard to reproduce the exact result ...
cooler
2 things to check:
finally cool2RangeCisPercent.py is added and tested - check out the jupyter notebook: https://nbviewer.jupyter.org/github/dekkerlab/digest-Hi-C/blob/master/cisRangePercent.ipynb
I tried to keep the same interface as the corresponding
hdf2RangeCisPercent.py- so this should be plug replaceable ...basically it does now exactly what Tyler's script was doing just using the streaming pixels approach from cooler - i.e. without ever dumping the whole dense matrix, just like here https://github.com/mirnylab/cooltools/blob/master/cooltools/coverage.py
so given the same input the results are going to be the same ...
problem is though, that
coolerbalances contact mao differently and it's hard to reproduce the exact result ...2 things to check: