search

jorvis / biocode

Bioinformatics code libraries and scripts
MIT License
504 stars 247 forks source link

Issue with convert prodigal output to standard GFF3 #83

Open jjuradoc opened 1 month ago

jjuradoc commented 1 month ago

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 commented 1 month ago

Do you think you could attach your input file here?

jjuradoc commented 1 month ago

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 importantehttps://aka.ms/LearnAboutSenderIdentification

Do you think you could attach your input file here?

— Reply to this email directly, view it on GitHubhttps://github.com/jorvis/biocode/issues/83#issuecomment-2425333473, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BMJAPLECTH6M52EETLZ5RDDZ4RETZAVCNFSM6AAAAABQI5M362VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRVGMZTGNBXGM. You are receiving this because you authored the thread.Message ID: @.***>

jorvis commented 1 month ago

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 commented 1 month ago

HI Joshua, sorry for that.

Please find attached the files here. Screenshot convert_prodigal_to_gff3.py.txt