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
    No fields configured for issues without a type.

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions