Error when running visualize

[pyongheng]

I am able to run annotate but get an error when I try to run visualize with the reference genome.
This is using the same genome as the previous issue (#38)

Visualize is able to run if I redo annotate without a reference genome.

(pseudofinder) ecbsu@ecbsu-Precision-7920-Tower:~/pseudofinder$ python3 pseudofinder.py visualize -log edit2_ref_gemino_log.txt -op test
2022-08-15 17:11:08	Starting Sleuth...
Traceback (most recent call last):
  File "/home/ecbsu/pseudofinder/pseudofinder.py", line 48, in <module>
    visualize.main()
  File "/home/ecbsu/pseudofinder/modules/visualize.py", line 130, in main
    settings_loop(args)  # Generates the data
  File "/home/ecbsu/pseudofinder/modules/visualize.py", line 42, in settings_loop
    genome = reannotate.prepare_data_for_analysis(args, None, log_file_dict)
  File "/home/ecbsu/pseudofinder/modules/reannotate.py", line 23, in prepare_data_for_analysis
    ref_genome = gbk_to_seqrecord_list(args, args.reference)
NameError: name 'gbk_to_seqrecord_list' is not defined

[mitchso]

Hi thank you for bringing this to my attention! The latest push should fix the error you are experiencing. Please let me know if you continue to have trouble running the visualize command on a genome annotated with sleuth.