AttributeError: 'GenomeViz' object has no attribute 'add_feature'

[Syutenjyo]

I am encountering an AttributeError when trying to use the add_feature method of the GenomeViz class in the pygenomeviz library.（portein-visualization） Here is the code snippet that I am using:

from pygenomeviz import GenomeViz
# Initialize GenomeViz
gv = GenomeViz()
# Add each annotation as a track
for ann in annotations:
    gv.add_feature(
        seq_id=ann['seq_id'],
        start=ann['start'],
        end=ann['end'],
        strand=ann['strand'],
        label=ann['annotation']
    )

The code results in the following error traceback:

Traceback (most recent call last):
  File "<stdin>", line 2, in <module>
AttributeError: 'GenomeViz' object has no attribute 'add_feature'

Environment Information:

• PhaBOX version: v2.1.10
• Python version: v3.12.3
• pyGenomeViz version: v1.5.0

[KennthShang]

Since this is an issue caused by the GenomeViz, maybe you should seek them for better help (we are not the same team and I know little about their implementation).

But I think maybe it is caused by the version of your pygenomeviz.

As a suggestion provided by the GPT-4o, a potential correction may be:

from pygenomeviz import GenomeViz

# Initialize GenomeViz
gv = GenomeViz()

# Add tracks for each sequence/annotation
for ann in annotations:
    # Add a feature track for each sequence ID
    track = gv.add_feature_track(seq_id=ann['seq_id'])
    
    # Add features (annotations) to the track
    track.add_feature(
        start=ann['start'],
        end=ann['end'],
        strand=ann['strand'],
        label=ann['annotation']
    )

Best,
Jiayu

[Syutenjyo]

Thank you for your prompt response and the suggested code. However, I am still encountering an error when using the code you provided. The error traceback I am getting is as follows:

Traceback (most recent call last):
  File "<stdin>", line 3, in <module>
TypeError: GenomeViz.add_feature_track() got an unexpected keyword argument 'seq_id'

Could you please tell me the version of the pygenomeviz package you are using? It might help me identify if the issue is related to version differences.

[KennthShang]

please check the API example in https://github.com/moshi4/pyGenomeViz

[KennthShang]

The version I am using is 1.4.1