Map quantitative values on the 3D model

[ghost]

I was following the steps in the tutorial to map quantitative values on the model run:

python ./scripts/map_parameter.py --pdb path/to/structure.pdb --bedgraph path/to/annotation.bedgraph --output path/to/output.pdb

The resultion is the same : 5kb
The bedgraph :
chr1 0 606 116.959
chr1 606 614 48.4495
chr1 614 976 116.959
chr2 0 19 22.8726
chr3 0 2 22.8726
chr4 0 18 22.8726

I received the following error :

Number of beads read from structure: 1015
Traceback (most recent call last):
File "/home/3d-genome-builder/./scripts/map_parameter.py", line 109, in
map_parameter(ARGS.pdb, ARGS.bedgraph, ARGS.output)
File "/home/3d-genome-builder/./scripts/map_parameter.py", line 82, in map_parameter
quantitative_parameter.columns = ["chromosome", "start", "end", "value"]
File "/home/miniconda3/envs/3DGB/lib/python3.10/site-packages/pandas/core/generic.py", line 6002, in setattr
return object.setattr(self, name, value)
File "pandas/_libs/properties.pyx", line 69, in pandas._libs.properties.AxisProperty.set
File "/home/miniconda3/envs/3DGB/lib/python3.10/site-packages/pandas/core/generic.py", line 730, in _set_axis
self._mgr.set_axis(axis, labels)
File "/home/miniconda3/envs/3DGB/lib/python3.10/site-packages/pandas/core/internals/managers.py", line 225, in set_axis
self._validate_set_axis(axis, new_labels)
File "/home/miniconda3/envs/3DGB/lib/python3.10/site-packages/pandas/core/internals/base.py", line 70, in _validate_set_axis
raise ValueError(
ValueError: Length mismatch: Expected axis has 1 elements, new values have 4 elements

[ghost]

@pierrepo @Thibault-Poinsignon can you help me to solve this error.

[pierrepo]

Hello @gayahaber
Given the error message you had, I suspect your bedgraph file has space-separated values instead of tab-separated values.
Could you please verify this point?

[ghost]

Hello @pierrepo,

No, my bedgraph is using a tab-seperated values. I writed again the bedgraph but still have the same error.

[pierrepo]

OK. Would you mind sharing your files with me (pdb and bedgraph files) by e-mail ([email protected]) or any means that you'll find suitable?

[ghost]

Yes no problem.