Load .hic file for Compartments and TADs detection?

[awezmm]

How can I load data from a .hic file for Compartments and TADs detection?

[david-castillo]

Hi,
We don't support .hic directly but you have two simple options:

1. Convert .hic to .mcool format for example with https://hicexplorer.readthedocs.io/en/latest/ and then use tadbit like:

from pytadbit import Chromosome, Experiment
cool_file = 'matrix=my_matrix.mcool'
exp = Experiment('exp1', hic_data=cool_file, resolution=my_resolution)
hic_data = exp.hic_data[0]

and then use the hic_data object to find compartments and tads like in https://3dgenomes.github.io/TADbit/tutorial/tutorial_8-Compartments_and_TADs_detection.html

2. Use straw (https://github.com/aidenlab/straw) or similar to create a text matrix and then build your own hic_data object like

from pytadbit import HiC_data
filename = 'my_matrix.dat'
resolution=my_resolution
size = int(full_size_in_bp/resolution)
my_chroms={'chr_name1':chr_size1_in_bp/resolution,'chr_name2':chr_size2_in_bp/resolution}
hic_tup = {int(int(line.split()[0])/resolution)+int(int(line.split()[1])/resolution)*size:int(line.split()[2])
            for line in open(filename)}

hic_data = HiC_data(hic_tup,size=size,resolution=resolution,chromosomes=my_chroms)

and then use the hic_data object to find compartments and tads like in https://3dgenomes.github.io/TADbit/tutorial/tutorial_8-Compartments_and_TADs_detection.html

The advantage of option 2 is that is faster than option 1 if you are just interested in a single chromosome.

Regards

[awezmm]

Great, thanks!