Skip to content

Error loading mcool file #383

@ericmalekos

Description

@ericmalekos

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'

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

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions