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Error when trying example scripts

See original GitHub issue

I am running python 2.7 on macOS. When I want to try the example script, i.e. from_genbank.py, I get the following error:

Traceback (most recent call last): File "with_plot.py", line 11, in <module> ax, levels = graphic_record.plot() File "/Library/Python/2.7/site-packages/dna_features_viewer/dna_features_viewer.py", line 234, in plot box_linewidth=box_linewidth, box_color=box_color File "/Library/Python/2.7/site-packages/dna_features_viewer/dna_features_viewer.py", line 207, in annotate_feature x1, y1, x2, y2 = get_text_box(text, margin=margin) File "/Library/Python/2.7/site-packages/dna_features_viewer/utils.py", line 39, in get_text_box renderer = text.axes.figure.canvas.get_renderer() AttributeError: 'FigureCanvasMac' object has no attribute 'get_renderer' Tobiass-Air:examples Tobias$ python from_genbank.py Traceback (most recent call last): File "from_genbank.py", line 3, in <module> graphic_record = BiopythonTranslator().translate_record("example_sequence.gb") File "/Library/Python/2.7/site-packages/dna_features_viewer/dna_features_viewer.py", line 468, in translate_record return grecord_class(sequence_length=len(record.seq), features=[ AttributeError: 'str' object has no attribute 'seq'

The other example scripts do not work either.

Issue Analytics

  • State:closed
  • Created 6 years ago
  • Comments:11 (6 by maintainers)

github_iconTop GitHub Comments

1reaction
Zulkocommented, May 28, 2017

That version if from 4 years ago, we may have something there. Can you try upgrading it ? This should install matplotlib 2.x (which as far as i know is retro-compatible so you shouldn’t have trouble with other projects):

sudo pip install --upgrade matplotlib
0reactions
Zulkocommented, May 29, 2017

What this means is that the latest changes and fixes on Github had not been pushed on PyPI, so that was an actual bug. Thanks for the report !

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