TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
Hello, I'm running into an error when I try to load an mcool file into an experiment object (as described in this answer).
>>> from pytadbit import Experiment
>>> exp = Experiment('exp1', hic_data='norm_THP1.Ctrl_100000.mcool', resolution=100000)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/public/home/emalekos/miniconda3/envs/tadbit/lib/python3.7/site-packages/pytadbit/experiment.py", line 198, in __init__
self.load_hic_data(hic_data, parser, **kw_descr)
File "/public/home/emalekos/miniconda3/envs/tadbit/lib/python3.7/site-packages/pytadbit/experiment.py", line 582, in load_hic_data
self.hic_data = read_matrix(hic_data, parser=parser, one=False)
File "/public/home/emalekos/miniconda3/envs/tadbit/lib/python3.7/site-packages/pytadbit/parsers/hic_parser.py", line 454, in read_matrix
not hic)
File "/public/home/emalekos/miniconda3/envs/tadbit/lib/python3.7/site-packages/pytadbit/parsers/cooler_parser.py", line 64, in parse_cooler
chrom = root_grp["chroms"]["name"].value
AttributeError: 'Dataset' object has no attribute 'value'
Hello, I'm running into an error when I try to load an mcool file into an experiment object (as described in this answer).
I set up my environment on 11/6/22 with
conda create -n tadbit python=3.7 r-base r-essentials r-devtools imp tadbit -c conda-forge -c bioconda