search

NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit
GNU General Public License v3.0
431 stars 52 forks source link

manage_functional_annotation deletes Name attribute #436

Closed Neato-Nick closed 3 months ago

Neato-Nick commented 4 months ago

Running a GFF through agat_sp_manage_functional_annotation.pl removes all Name attributes from a GFF. One possibility: Maybe it's because I'm only using interproscan results, and not integrating blast hits?

General:

To Reproduce

$ cat FKS1.gff3
scaffold00002   Liftoff gene    2088186 2093852 .   -   .   ID=B9J08_2928;Name=1%2C3-beta-glucan synthase component FKS1;old_locus_tag=B9J08_000964
scaffold00002   Liftoff mRNA    2088186 2093852 .   -   .   ID=B9J08_2928.1;Parent=B9J08_2928;Name=1%2C3-beta-glucan synthase component FKS1;Note=B8441v2:B9J08_000964T0
scaffold00002   Liftoff exon    2088186 2093852 .   -   0   ID=B9J08_2928.1-exon1;Parent=B9J08_2928.1;Note=B8441v2:B9J08_000964.exon1
scaffold00002   Liftoff CDS 2088186 2093852 .   -   0   ID=B9J08_2928.1-cds1;Parent=B9J08_2928.1;Note=B8441v2:cds.B9J08_000964
$ cat ipr.FKS1.tsv
B9J08_2928.1    fb80cc001e72d0cabe21f912d87a447e    1888    Pfam    PF02364 1,3-beta-glucan synthase component  804 1635    0.0 T   08-02-2024  IPR003440   Glycosyl transferase, family 48 GO:0000148(InterPro)|GO:0003843(InterPro)|GO:0006075(InterPro)|GO:0016020(InterPro) -
B9J08_2928.1    fb80cc001e72d0cabe21f912d87a447e    1888    Pfam    PF14288 1,3-beta-glucan synthase subunit FKS1, domain-1 297 404 7.9E-30 T   08-02-2024  IPR026899   1,3-beta-glucan synthase component FKS1-like, domain-1  -   -
$ agat_sp_manage_functional_annotation.pl -f FKS1.gff3 -i ipr.FKS1.tsv -o FKS1.ipr
$ cat FKS1.ipr/FKS1.gff3
##gff-version 3
scaffold00002   Liftoff gene    2088186 2093852 .   -   .   ID=B9J08_2928;old_locus_tag=B9J08_000964
scaffold00002   Liftoff mRNA    2088186 2093852 .   -   .   ID=B9J08_2928.1;Parent=B9J08_2928;Dbxref=-,InterPro:IPR003440,InterPro:IPR026899,Pfam:PF02364,Pfam:PF14288;Note=B8441v2:B9J08_000964T0;Ontology_term=GO:0000148(InterPro),GO:0003843(InterPro),GO:0006075(InterPro),GO:0016020(InterPro)
scaffold00002   Liftoff exon    2088186 2093852 .   -   0   ID=B9J08_2928.1-exon1;Parent=B9J08_2928.1;Note=B8441v2:B9J08_000964.exon1
scaffold00002   Liftoff CDS 2088186 2093852 .   -   0   ID=B9J08_2928.1-cds1;Parent=B9J08_2928.1;Note=B8441v2:cds.B9J08_000964

Expected behavior The Name= attribute should be retained, and if --pcds is used, should also be copied from mRNA to CDS.

Additional context Happens whether or not --pcds is used. I added blast result info, and the Name attribute is still stripped. My example test case unfortunately didn't have any hits so it wasn't ideal.

0 gene names have been retrieved in the blast file. 0 gene names have been successfully inferred. Among them there are 0 names that are shared at least per two genes for a total of 0 genes.