AttributeError: 'Gene' object has no attribute 'add_CDS'

[jorvis]

AttributeError: 'Gene' object has no attribute 'add_CDS'

[jorvis]

Yeah, NCBI is putting out some strange GFF here which has exon/CDS features which are directly associated with a gene rather than any type of RNA. This goes against what model organism databases (from which GFF sprung) have done, but I suppose GBK and Ensembl are big enough that we'll have to modify to handle whatever they export, even if it is incorrect.

[jorvis]

Hmm, checked their format doc and it looks like within there your file also validates what they say they accept. Their own documentation holds the gene -> RNA -> exon/CDS parentage.

https://www.ncbi.nlm.nih.gov/genbank/genomes_gff/#formatting

[jorvis]

Closing this since it appears to be an issue with the file not being in NCBI's published format.

[PlantDr430]

Hmm okay. It is an older file, so perhaps they had different formats back then and recently updated their standards.

…

On Sun, Jul 7, 2019 at 8:38 PM Joshua Orvis ***@***.***> wrote: Closing this since it appears to be an issue with the file not being in NCBI's published format. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#62?email_source=notifications&email_token=AHB5CPZ2JFZQAHNGOEKB6GTP6KSD7A5CNFSM4H6NF3A2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZLZ5IY#issuecomment-509058723>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHB5CPZVZV5LCPV2X7EZGXLP6KSD7ANCNFSM4H6NF3AQ> .