agat_sp_manage_functional_annotation.pl formatting issue

[nbisweden]

agat_sp_manage_functional_annotation.pl formatting issue

[Juke34]

Hi, any reason you opened the issue in the GAAS repo rather the AGAT repo?

No worries, they are just warning. Indeed for many years Augustus and subsequent tools as TSEBRA create feature without mandatory attributes requested by the format (here the transcript feature line).
AGAT handles this perfectly well.
In such case AGAT uses a sequential approach, which means all level3 features (exon, CDS...) are llinked o the last level2 feature (transcript) met when reading the file from top to bottom.
Look at the output for the example you provided, you will see it should be fine.

[JuliaLopezDelgado]

Hello,

Sorry for posting on the wrong repo!

Thanks for letting me know about the warning. It does seem like it ran okay when I check the output folder.

Many thanks,
Julia