Derived_from not checked

[nathanhaigh]

TAIR10 GFF file (ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_gff3/TAIR10_GFF3_genes.gff) contains the attribute Derived_from which references ransposable element features not defined in the GFF file.

I think that gt gff3 should throw an error (perhaps only when -checkids is specified) in such situations. In addition, perhaps gt gff3validator should throw an error?

curl ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_gff3/TAIR10_GFF3_genes.gff \
| sed '1i ##gff-version 3' \
| sed -r 's/Index/index/g' \
| gt gff3 -retainids \
| git_repos/gff3sort/gff3sort.pl /dev/stdin \
| bgzip \
> TAIR10_GFF3_genes.gff3.gz
gt gff3validator TAIR10_GFF3_genes.gff3.gz

[gordon]

Although this requirement (Derives_from references should exist) is not explicitly mentioned in the GFF3 it would make sense to add this check.

I think the best solution would be to add a -checkderivesfrom option to gt gff3 and gt gff3validator which implies -checkids.

Any volunteers?