Error when running gff3_ID_generator.py

[B203712-2021]

Error when running gff3_ID_generator.py

[mpoelchau]

Sorry you're having trouble with the script. Could you attach a snippet of the gff3 file to help troubleshoot (or the whole file if it's not too big/private)?

[B203712-2021]

I'm so sorry for my late response. I've tried to submitted all the two gff and gff3 files to my github becuase they're too large, and I hope you can see them. All the two files will got errors when doing gff3_ID_generator.py (the gff3 files) or gff_to_fasta. Thank you for your reponse and hope for any advice how can I fix the error.
https://github.com/B203712-2021/Project

[mpoelchau]

Hi @B203712-2021 ,

The problem is that your gff3 file has sequence-region directive lines where the end coordinate is "None", e.g.
##sequence-region est_AJ558253.1.mrna1 1 None

The program assumes that the end coordinate is a number (not a bad assumption but I admit the GFF3 spec doesn't explicitly state that it has to be a number, https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md). Do you know why the end coordinate is 'None'?

In the meantime, you can just remove the sequence-directive lines to get the program to work.

[mpoelchau]

@B203712-2021 did removing/changing the sequence region directive work for you?

I'm closing this issue, but feel free to re-open if that didn't help.