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gatech-genemark / Mgcod

Tool for recognizing genetic codes (incl. multiple genetic codes in phage genomes) and genetic-code-informed annotation of coding regions in prokaryotic sequences
GNU General Public License v3.0
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Error in plotting #2

Closed Thexiyang closed 1 year ago

Thexiyang commented 2 years ago

During running this software, I came across this issue. Any suggestion on how to solve this? Thanks！

Traceback (most recent call last):
  File "/Mgcod/bin/mgcod.py", line 185, in <module>
    main(sys.argv[1:])
  File "Mgcod/bin/mgcod.py", line 152, in main
    if pipeline.predicted_switch_regions[contig] is None:
TypeError: 'NoneType' object is not subscriptable
AaronRuben commented 2 years ago

Hi,

Could be a problem with the pandas or numpy version. Which versions are you using?

If you could share your input file and the command you used, I can try to reproduce the error and see what's causing it.

Best, Aaron

AaronRuben commented 1 year ago

Closing due to inactivity. Please, re-open if this issue persists.

shujieH commented 1 year ago

Hi, Aaron

Thanks for providing us with this excellent tool! During the runtime, I met the same problem as above. And the versions of

pandas numpy, which I used were v1.2.4 and v1.18.1, respectively. Here is my input file and input command. Please help me

solve this problem. Thank you!

test.zip

mgcod.py -i test.fa -r --isoforms -v -m ./plots -p test_mgm_result -o test_results

捕获

Best wishes, Shujie.

AaronRuben commented 1 year ago

Hi Shujie,

Thanks for using Mgcod and glad to hear that you find useful.

What version of Mgcod are you running? I could reproduce your error with version 1.0.0. However, it seems to be fixed in version 1.0.1. Depending on how you installed Mgcod, you can update it by running conda update mgcod or git pull.

Let me know if the issue persists after updating Mgcod.

Best, Aaron

shujieH commented 1 year ago

Hi, Aaron

Thank you for your prompt reply!

According to your suggestion, I installed the latest version of Mgcod (v1.0.1) with conda, and finally solved the above problem smoothly. Thanks again for your kind help.

All Best, Shujie