Error running the tutorial

[raphaeltrevizani]

I get the following error when I run the tutorial. What am I doing wrong?

$ python GIANA4.1.py -f data/tutorial.txt
Traceback (most recent call last):
  File "/home/trevizani/prog/GIANA/GIANA4.1.py", line 39, in <module>
    from query import *
  File "/home/trevizani/prog/GIANA/query.py", line 6, in <module>
    from GIANA4 import *
  File "/home/trevizani/prog/GIANA/GIANA4.py", line 54, in <module>
    vv=blosum62[kk]
       ~~~~~~~~^^^^
  File "/home/trevizani/prog/GIANA/venv/lib/python3.11/site-packages/Bio/Align/substitution_matrices/__init__.py", line 146, in __getitem__
    value = numpy.ndarray.__getitem__(self, key)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: arrays used as indices must be of integer (or boolean) type

[s175573]

Are you using Python3 or Python2?

[raphaeltrevizani]

python 3.11.5

[4C69204C696E]

Hi I had the same problem, have you solved it yet?

[raphaeltrevizani]

No, I gave up.

On Tue, Jan 9, 2024, 19:37 4C69204C696E @.***> wrote:

Hi I had the same problem, have you solved it yet?

— Reply to this email directly, view it on GitHub https://github.com/s175573/GIANA/issues/10#issuecomment-1884138898, or unsubscribe https://github.com/notifications/unsubscribe-auth/AILJ4IJATCA3ACVRG3VA723YNYEILAVCNFSM6AAAAAA5UWL2G6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBUGEZTQOBZHA . You are receiving this because you authored the thread.Message ID: @.***>

[4C69204C696E]

No, I gave up. … On Tue, Jan 9, 2024, 19:37 4C69204C696E @.> wrote: Hi I had the same problem, have you solved it yet? — Reply to this email directly, view it on GitHub <#10 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AILJ4IJATCA3ACVRG3VA723YNYEILAVCNFSM6AAAAAA5UWL2G6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBUGEZTQOBZHA . You are receiving this because you authored the thread.Message ID: @.>

Thanks I'll look for another way and if it worls I'll get back to you.

[s175573]

Apologies for the delay. I've updated the code to accommodate the changes in python packages. Please feel free to try again.

[4C69204C696E]

Hi there, I tried again and encountered an issue while running the command "python GIANA4.1.py -f tutorial.txt." The error traceback is as follows:

Traceback (most recent call last):
  File "GIANA-master/GIANA4.1.py", line 1257, in <module>
    main()
  File "GIANA-master/GIANA-master/GIANA4.1.py", line 1241, in main
    VScore[(ww[0], ww[1])] = int(ww[2]) / 20
ValueError: invalid literal for int() with base 10: '80.0'

Could you provide guidance on what might be causing this issue? I appreciate your assistance.

[s175573]

Just updated. Can you please try again?

From: 4C69204C696E @.> Date: Friday, January 12, 2024 at 9:19 AM To: s175573/GIANA @.> Cc: Bo Li @.>, Comment @.> Subject: Re: [s175573/GIANA] Error running the tutorial (Issue #10) EXTERNAL MAIL

Hi there, I tried again and encountered an issue while running the command "python GIANA4.1.py -f tutorial.txt." The error traceback is as follows:

Traceback (most recent call last):

File "GIANA-master/GIANA4.1.py", line 1257, in

main()

File "GIANA-master/GIANA-master/GIANA4.1.py", line 1241, in main

VScore[(ww[0], ww[1])] = int(ww[2]) / 20

ValueError: invalid literal for int() with base 10: '80.0'

Could you provide guidance on what might be causing this issue? I appreciate your assistance.

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/s175573/GIANA/issues/10*issuecomment-1889330978__;Iw!!MznTZTSvDXGV0Co!GZgvQJp176OIF56qqJdXqRPTlLd7ld2xz4Lnsgp1GhUanSGR2sgZCx4wh66MqfgmWRCyMRLI232wIYEeDAhi2w2RvbqPCYs$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AKWYQC3Y2F5RE4S5QRK4QHDYOFA5JAVCNFSM6AAAAAA5UWL2G6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBZGMZTAOJXHA__;!!MznTZTSvDXGV0Co!GZgvQJp176OIF56qqJdXqRPTlLd7ld2xz4Lnsgp1GhUanSGR2sgZCx4wh66MqfgmWRCyMRLI232wIYEeDAhi2w2Rg3CDYnc$. You are receiving this because you commented.Message ID: @.***> CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.

---

UT Southwestern

Medical Center

The future of medicine, today.

[4C69204C696E]

Just updated. Can you please try again? From: 4C69204C696E @.> Date: Friday, January 12, 2024 at 9:19 AM To: s175573/GIANA @.> Cc: Bo Li @.>, Comment @.> Subject: Re: [s175573/GIANA] Error running the tutorial (Issue #10) EXTERNAL MAIL Hi there, I tried again and encountered an issue while running the command "python GIANA4.1.py -f tutorial.txt." The error traceback is as follows: Traceback (most recent call last): File "GIANA-master/GIANA4.1.py", line 1257, in main() File "GIANA-master/GIANA-master/GIANA4.1.py", line 1241, in main VScore[(ww[0], ww[1])] = int(ww[2]) / 20 ValueError: invalid literal for int() with base 10: '80.0' Could you provide guidance on what might be causing this issue? I appreciate your assistance. — Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/s175573/GIANA/issues/10*issuecomment-1889330978__;Iw!!MznTZTSvDXGV0Co!GZgvQJp176OIF56qqJdXqRPTlLd7ld2xz4Lnsgp1GhUanSGR2sgZCx4wh66MqfgmWRCyMRLI232wIYEeDAhi2w2RvbqPCYs$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AKWYQC3Y2F5RE4S5QRK4QHDYOFA5JAVCNFSM6AAAAAA5UWL2G6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBZGMZTAOJXHA__;!!MznTZTSvDXGV0Co!GZgvQJp176OIF56qqJdXqRPTlLd7ld2xz4Lnsgp1GhUanSGR2sgZCx4wh66MqfgmWRCyMRLI232wIYEeDAhi2w2Rg3CDYnc$. You are receiving this because you commented.Message ID: @.***> CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. … ____ UT Southwestern Medical Center The future of medicine, today.

I tired again and the issue has been solved. Thank you.