Issue with convert prodigal output to standard GFF3

[jjuradoc]

Hi,

I want to convert the Prodigal output to standard GFF3 using the command: convert_prodigal_to_gff3.py -i unit2_new_genome.prodigal.gff -o unit2_new_genome.prodigal.gff3

I obtain this error message:

Traceback (most recent call last):
File "/home/jjuradoc/class/myenv/bin/convert_prodigal_to_gff3.py", line 66, in
main()
File "/home/jjuradoc/class/myenv/bin/convert_prodigal_to_gff3.py", line 53, in main
id, annotation = m.groups()
^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'groups'

What can I do in this case? thank you in advance

[jorvis]

Do you think you could attach your input file here?

[jjuradoc]

Hi Joshua, Thank you for replying to my message. Please find attached a screenshot of the message I got and of the input file. Thank you. Sincerely, Juan Jurado [Email signature image for Schulich] Juan Jurado-Coronel MSc in Biotechnology, BSc in Biology PhD in Neuroscience Student - Duennwald Lab University of Western Ontario MSB415 (Lab) London, ON, Canada, N6A 5C1 E-mail: ***@***.***

…

________________________________ De: Joshua Orvis ***@***.***> Enviado: domingo, 20 de octubre de 2024 20:41 Para: jorvis/biocode ***@***.***> Cc: Juan Jurado Coronel ***@***.***>; Author ***@***.***> Asunto: Re: [jorvis/biocode] Issue with convert prodigal output to standard GFF3 (Issue #83) No suele recibir correo electrónico de ***@***.*** Por qué es esto importante<https://aka.ms/LearnAboutSenderIdentification> Do you think you could attach your input file here? — Reply to this email directly, view it on GitHub<#83 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BMJAPLECTH6M52EETLZ5RDDZ4RETZAVCNFSM6AAAAABQI5M362VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRVGMZTGNBXGM>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[jorvis]

Juan -

I don't believe you can attach something when replying to the issue via e-mail. Could you please try again using GitHub in your browser?

[jjuradoc]

HI Joshua, sorry for that.

Please find attached the files here.

convert_prodigal_to_gff3.py.txt