Annotation GFFs with duplicate ID records

[sammyjava]

OK, I'm consolidating this issue into one since there are a lot of these GFFs with duplicate IDs. Fix 'em and check 'em off!

• [x] Gyeongwon.gnm3.ann1
• [x] Amiga.gnm1.ann1
• [x] ICC4958.gnm2.ann1
• [x] Xiabao_II.gnm1.ann1
• [x] Zh13.gnm2.ann1
• [x] Tifrunner.gnm1.ann1
• [x] Tifrunner.gnm2.ann1
• [x] XinJiangDaYe.gnm1.ann1.RKB9
• [x] VC1973A.gnm7.ann1.RWBG

[StevenCannon-USDA]

Fwiw, I am planning to start on these tomorrow (Groundhog Day; hope that doesn't augur ill)

[adf-ncgr]

OK, I think these should now be handled. One potential remaining issue is with Zh13.gnm2.ann1 which has some gene features that have the same ID value as child miRNA_primary_transcript features. I think it doesn't bother intermine if IDs are the same, as long as they are associated with objects of different types; but it might still bother someone. In any case, let me know if any loading issues remain with any of these.

[sammyjava]

Correct, in fact we typically have proteins and transcripts with the same ID (from different files, but mine loaders don't care about that). It's object.class + object.primaryIdentifer that must be unique (for Annotatables).

[sammyjava]

sigh I'll list 'em one by one in following comments.

[sammyjava]

[shokin@lis ~]$ validate-annotation-collection v2/Vigna/angularis/annotations/Gyeongwon.gnm3.ann1.3Nz5/

Validating vigan collection Gyeongwon.gnm3.ann1.3Nz5

• vigan.Gyeongwon.gnm3.ann1.3Nz5.gene_models_main.gff3.gz

  INVALID: vigan.Gyeongwon.gnm3.ann1.3Nz5.gene_models_main.gff3.gz record ID is duplicate of one already read:

  INVALID: vigan.Gyeongwon.gnm3.SuperScaf_10 vigan.Gyeongwon.gnm3.ann1.a1 five_prime_UTR -80053 -79912 0.0 . ID=vigan.Gyeongwon.gnm3.ann1.Vang0010ss00060.1:five_prime_utr;Parent=vigan.Gyeongwon.gnm3.ann1.Vang0010ss00060.1

• vigan.Gyeongwon.gnm3.ann1.3Nz5.protein.faa.gz
• vigan.Gyeongwon.gnm3.ann1.3Nz5.protein_primary.faa.gz
• vigan.Gyeongwon.gnm3.ann1.3Nz5.cds.fna.gz
• vigan.Gyeongwon.gnm3.ann1.3Nz5.cds_primary.fna.gz
• vigan.Gyeongwon.gnm3.ann1.3Nz5.mrna.fna.gz
• vigan.Gyeongwon.gnm3.ann1.3Nz5.mrna_primary.fna.gz x optional iprscan.gff3.gz file is not present.
• vigan.Gyeongwon.gnm3.ann1.3Nz5.legfed_v1_0.M65K.gfa.tsv.gz
• vigan.Gyeongwon.gnm3.ann1.3Nz5.legfed_v1_0.M65K.pathway.tsv.gz x optional phytozome_10_2.HFNR.gfa.tsv.gz file is not present.

[sammyjava]

Different issue but I'll put it here since we're trying to get these annotation collections to validate.

Validating arahy collection Tifrunner.gnm2.ann1.4K0L

• arahy.Tifrunner.gnm2.ann1.4K0L.gene_models_main.gff3.gz
• arahy.Tifrunner.gnm2.ann1.4K0L.protein.faa.gz
• arahy.Tifrunner.gnm2.ann1.4K0L.protein_primary.faa.gz
• arahy.Tifrunner.gnm2.ann1.4K0L.cds.fna.gz
• arahy.Tifrunner.gnm2.ann1.4K0L.cds_primary.fna.gz
• arahy.Tifrunner.gnm2.ann1.4K0L.mrna.fna.gz
• arahy.Tifrunner.gnm2.ann1.4K0L.mrna_primary.fna.gz x optional iprscan.gff3.gz file is not present.
• arahy.Tifrunner.gnm2.ann1.4K0L.legfed_v1_0.M65K.gfa.tsv.gz

  INVALID: GFA file contains gene ID arahy.Tifrunner.gnm2.ann1.B9P371 that is not present in the gene models GFF file.

• arahy.Tifrunner.gnm2.ann1.4K0L.legfed_v1_0.M65K.pathway.tsv.gz x optional phytozome_10_2.HFNR.gfa.tsv.gz file is not present.

[sammyjava]

OK, that's it, seven out of nine isn't too bad.

[adf-ncgr]

OK, the issue with Gyeongwon.gnm3.ann1 should be fixed, I'd not realized on the first one that some non-CDS features were sometimes at issue as well. Will look into the remaining gfa issues, but not immediately.

[sammyjava]

I expect it can be any type. It validates, thanks! I'll close this since we do have the specific issue on the GFA non-conformity.